CDK5RAP1

Functionⁱ

Methylthiotransferase that catalyzes the conversion of N6-(dimethylallyl)adenosine (i₆A) to 2-methylthio-N6-(dimethylallyl)adenosine (ms₂i₆A) at position 37 (adjacent to the 3'-end of the anticodon) of four mitochondrial DNA-encoded tRNAs (Ser(UCN), Phe, Tyr and Trp) (PubMed:22422838, PubMed:25738458, PubMed:28981754). Essential for efficient and highly accurate protein translation by the ribosome (PubMed:22422838, PubMed:25738458, PubMed:28981754). Specifically inhibits CDK5 activation by CDK5R1 (PubMed:11882646). Essential for efficient mitochondrial protein synthesis and respiratory chain; shows pathological consequences in mitochondrial disease (PubMed:25738458).4 Publications

Caution

CDK5RAP1 was proposed to act on both nuclear and mitochondrial RNA (PubMed:22422838). However, another study shows that ms2i6A is a mitochondrial tRNA specific modification and is absent from nuclear encoded RNA species, implying that there is no methylthiotransferase activity on nuclear RNA (PubMed:28981754).2 Publications

Catalytic activityⁱ

[sulfur carrier]-SH
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
+
AH₂
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Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+
N⁶-dimethylallyladenosine³⁷ in tRNA
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Search chemical reactions in Rhea for this molecule.
+ 2
S-adenosyl-L-methionine
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
=
2-methylsulfanyl-N⁶-dimethylallyladenosine³⁷ in tRNA
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Search chemical reactions in Rhea for this molecule.
+
5'-deoxyadenosine
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Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+
[sulfur carrier]-H
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Search chemical reactions in Rhea for this molecule.
+
A
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+ 2
H⁺
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Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+
L-methionine
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
+
S-adenosyl-L-homocysteine
Search proteins in UniProtKB for this molecule.
Search chemical reactions in Rhea for this molecule.
See the description of this molecule in ChEBI.
2 Publications
Manual assertion inferred by curator fromⁱ
- Ref.10
  "The CDK5 repressor CDK5RAP1 is a methylthiotransferase acting on nuclear and mitochondrial RNA."
  Reiter V., Matschkal D.M., Wagner M., Globisch D., Kneuttinger A.C., Mueller M., Carell T.
  Nucleic Acids Res. 40:6235-6240(2012) [PubMed] [Europe PMC] [Abstract]
  Cited for: FUNCTION, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY.
- Ref.11
  "Cdk5rap1-mediated 2-methylthio modification of mitochondrial tRNAs governs protein translation and contributes to myopathy in mice and humans."
  Wei F.Y., Zhou B., Suzuki T., Miyata K., Ujihara Y., Horiguchi H., Takahashi N., Xie P., Michiue H., Fujimura A., Kaitsuka T., Matsui H., Koga Y., Mohri S., Suzuki T., Oike Y., Tomizawa K.
  Cell Metab. 21:428-442(2015) [PubMed] [Europe PMC] [Abstract]
  Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF CYS-258; CYS-262 AND CYS-265.
EC:
2.8.4.3
- Search proteins in UniProtKB for this EC number.
- See the description of this EC number in ENZYME.
2 Publications
Manual assertion inferred by curator fromⁱ
- Ref.10
  "The CDK5 repressor CDK5RAP1 is a methylthiotransferase acting on nuclear and mitochondrial RNA."
  Reiter V., Matschkal D.M., Wagner M., Globisch D., Kneuttinger A.C., Mueller M., Carell T.
  Nucleic Acids Res. 40:6235-6240(2012) [PubMed] [Europe PMC] [Abstract]
  Cited for: FUNCTION, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY.
- Ref.11
  "Cdk5rap1-mediated 2-methylthio modification of mitochondrial tRNAs governs protein translation and contributes to myopathy in mice and humans."
  Wei F.Y., Zhou B., Suzuki T., Miyata K., Ujihara Y., Horiguchi H., Takahashi N., Xie P., Michiue H., Fujimura A., Kaitsuka T., Matsui H., Koga Y., Mohri S., Suzuki T., Oike Y., Tomizawa K.
  Cell Metab. 21:428-442(2015) [PubMed] [Europe PMC] [Abstract]
  Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF CYS-258; CYS-262 AND CYS-265.
This reaction proceeds in the
forward
Search for this reaction in UniProtKB.
See the description of this reaction in Rhea.
1 Publication
Manual assertion inferred by curator fromⁱ
- Ref.10
  "The CDK5 repressor CDK5RAP1 is a methylthiotransferase acting on nuclear and mitochondrial RNA."
  Reiter V., Matschkal D.M., Wagner M., Globisch D., Kneuttinger A.C., Mueller M., Carell T.
  Nucleic Acids Res. 40:6235-6240(2012) [PubMed] [Europe PMC] [Abstract]
  Cited for: FUNCTION, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY.
1 Publication
Manual assertion based on experiment inⁱ
- Ref.11
  "Cdk5rap1-mediated 2-methylthio modification of mitochondrial tRNAs governs protein translation and contributes to myopathy in mice and humans."
  Wei F.Y., Zhou B., Suzuki T., Miyata K., Ujihara Y., Horiguchi H., Takahashi N., Xie P., Michiue H., Fujimura A., Kaitsuka T., Matsui H., Koga Y., Mohri S., Suzuki T., Oike Y., Tomizawa K.
  Cell Metab. 21:428-442(2015) [PubMed] [Europe PMC] [Abstract]
  Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF CYS-258; CYS-262 AND CYS-265.
direction.
Source:
Rhea
Search for this reaction in UniProtKB.
See the description of this reaction in Rhea.
. Show »« Hide
[sulfur carrier]-SH
thiol group
zoom
+
AH₂
+
N⁶-dimethylallyladenosine³⁷ in tRNA
N⁶-(3-methylbut-2-en-1-yl)-adenosine 5'-phosphate residue
zoom
+
2
S-adenosyl-L-methionine
zoom
=
2-methylsulfanyl-N⁶-dimethylallyladenosine³⁷ in tRNA
N⁶-(3-methylbut-2-en-1-yl)-2-(methylsulfanyl)adenosine 5'-phosphate residue
zoom
+
5'-deoxyadenosine
zoom
+
[sulfur carrier]-H
H group
zoom
+
A
+
2
H⁺
+
L-methionine
zoom
+
S-adenosyl-L-homocysteine
zoom

Cofactorⁱ

[4Fe-4S] clusterPROSITE-ProRule annotationNote: Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.PROSITE-ProRule annotation

Sites

Feature key	Position(s)	DescriptionActions	Length
Metal bindingⁱ	109	Iron-sulfur (4Fe-4S)PROSITE-ProRule annotation	1
Metal bindingⁱ	145	Iron-sulfur (4Fe-4S)PROSITE-ProRule annotation	1
Metal bindingⁱ	183	Iron-sulfur (4Fe-4S)PROSITE-ProRule annotation	1
Metal bindingⁱ	258	Iron-sulfur (4Fe-4S-S-AdoMet)By similarity	1
Metal bindingⁱ	262	Iron-sulfur (4Fe-4S-S-AdoMet)By similarity	1
Metal bindingⁱ	265	Iron-sulfur (4Fe-4S-S-AdoMet)By similarity	1

GO - Molecular functionⁱ

Complete GO annotation on QuickGO ...

GO - Biological processⁱ

Complete GO annotation on QuickGO ...

Keywordsⁱ

Molecular function	Transferase
Biological process	tRNA processing
Ligand	4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

PathwayCommonsⁱ	Q96SZ6

PathwayCommonsⁱ

Q96SZ6

Names & Taxonomyⁱ

Protein namesⁱ	Recommended name: Mitochondrial tRNA methylthiotransferase CDK5RAP12 Publications (EC:2.8.4.32 Publications) Alternative name(s): CDK5 activator-binding protein C42 CDK5 regulatory subunit-associated protein 1 mt-tRNA-2-methylthio-N6-dimethylallyladenosine synthase mt-tRNA-N6-(dimethylallyl)adenosine(37) methylthiotransferase
Gene namesⁱ	Name:CDK5RAP1Imported Synonyms:C20orf34 ORF Names:CGI-05, HSPC167
Organismⁱ	Homo sapiens (Human)
Taxonomic identifierⁱ	9606 [NCBI]
Taxonomic lineageⁱ	cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Dipnotetrapodomorpha › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Boreoeutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo
Proteomesⁱ	UP000005640 Componentⁱ: Chromosome 20

Organism-specific databases

Human Gene Nomenclature Database More...HGNCⁱ	HGNC:15880, CDK5RAP1
MIMⁱ	608200, gene
neXtProtⁱ	NX_Q96SZ6
VEuPathDBⁱ	HostDB:ENSG00000101391.20

Keywords - Cellular componentⁱ

Mitochondrion

Pathology & Biotechⁱ

Mutagenesis

Feature key	Position(s)	DescriptionActions	Length
Mutagenesisⁱ	258	C → A: Loss of mitochondrial tRNAs methylthiotransferase activity; when associated with A-262 and A-265. 1 Publication	1
Mutagenesisⁱ	262	C → A: Loss of mitochondrial tRNAs methylthiotransferase activity; when associated with A-258 and A-265. 1 Publication	1
Mutagenesisⁱ	265	C → A: Loss of mitochondrial tRNAs methylthiotransferase activity; when associated with A-258 and A-262. 1 Publication	1

Organism-specific databases

DisGeNET More...DisGeNETⁱ	51654
Open Targets More...OpenTargetsⁱ	ENSG00000101391
PharmGKBⁱ	PA26313

Miscellaneous databases

Pharosⁱ	Q96SZ6, Tbio

Pharosⁱ

Q96SZ6, Tbio

Genetic variation databases

BioMutaⁱ	CDK5RAP1
DMDMⁱ	32129446

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Transit peptideⁱ	1 – 33	MitochondrionSequence analysisAdd BLAST		33
ChainⁱPRO_0000141764	34 – 601	Mitochondrial tRNA methylthiotransferase CDK5RAP1Sequence analysisAdd BLAST		568

Proteomic databases

EPDⁱ	Q96SZ6
jPOSTⁱ	Q96SZ6
MassIVEⁱ	Q96SZ6
MaxQB - The MaxQuant DataBase More...MaxQBⁱ	Q96SZ6
PaxDbⁱ	Q96SZ6
PeptideAtlas More...PeptideAtlasⁱ	Q96SZ6
PRIDEⁱ	Q96SZ6
ProteomicsDBⁱ	65981 78165 [Q96SZ6-1] 78166 [Q96SZ6-2] 78167 [Q96SZ6-3] 78168 [Q96SZ6-4]

PTM databases

iPTMnetⁱ	Q96SZ6
PhosphoSitePlusⁱ	Q96SZ6

Expressionⁱ

Tissue specificityⁱ

Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas (PubMed:10721722). Expressed in neurons of central nervous tissue (PubMed:10721722, PubMed:11882646).2 Publications

Isoform 5:

Mainly expressed in brain, placenta and testis.

Isoform 6:

High expression in placenta and lung.

Gene expression databases

Bgeeⁱ	ENSG00000101391, Expressed in small intestine Peyer's patch and 238 other tissues
ExpressionAtlasⁱ	Q96SZ6, baseline and differential
Genevisibleⁱ	Q96SZ6, HS

Organism-specific databases

Human Protein Atlas More...HPAⁱ	ENSG00000101391, Low tissue specificity

HPAⁱ

ENSG00000101391, Low tissue specificity

Interactionⁱ

Subunit structureⁱ

Interacts with CDK5R1 (p35 form). CDK5RAP1, CDK5RAP2 and CDK5RAP3 show competitive binding to CDK5R1.

Forms a complex with CDK5R1 and CDK5.

1 Publication

GO - Molecular functionⁱ

protein kinase binding
Source: UniProtKB
Non-traceable author statementⁱ
- Ref.8
  "Cloning of three novel neuronal Cdk5 activator binding proteins."
  Ching Y.-P., Qi Z., Wang J.H.
  Gene 242:285-294(2000) [PubMed] [Europe PMC] [Abstract]
  Cited for: TISSUE SPECIFICITY.

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

BioGRIDⁱ	119661, 63 interactors
IntActⁱ	Q96SZ6, 18 interactors
STRINGⁱ	9606.ENSP00000217372

Miscellaneous databases

RNActⁱ	Q96SZ6, protein

RNActⁱ

Q96SZ6, protein

Family & Domainsⁱ

Domains and Repeats

Feature key	Position(s)	DescriptionActions	Length
Domainⁱ	100 – 220	MTTase N-terminalPROSITE-ProRule annotationAdd BLAST	121
Domainⁱ	244 – 512	Radical SAM corePROSITE-ProRule annotationAdd BLAST	269
Domainⁱ	515 – 590	TRAMPROSITE-ProRule annotationAdd BLAST	76

Sequence similaritiesⁱ

Belongs to the methylthiotransferase family. MiaB subfamily.Curated

Keywords - Domainⁱ

Transit peptide

Phylogenomic databases

eggNOGⁱ	KOG2492, Eukaryota
Ensembl GeneTree More...GeneTreeⁱ	ENSGT00940000160361
HOGENOMⁱ	CLU_018697_2_1_1
InParanoidⁱ	Q96SZ6
OMAⁱ	CEHFHIP
Database of Orthologous Groups More...OrthoDBⁱ	835984at2759
PhylomeDBⁱ	Q96SZ6
TreeFamⁱ	TF101033

Family and domain databases

Gene3Dⁱ	3.40.50.12160, 1 hit 3.80.30.20, 1 hit
HAMAPⁱ	MF_01864, tRNA_metthiotr_MiaB, 1 hit
InterProⁱ	View protein in InterPro IPR006638, Elp3/MiaB/NifB IPR005839, Methylthiotransferase IPR020612, Methylthiotransferase_CS IPR013848, Methylthiotransferase_N IPR038135, Methylthiotransferase_N_sf IPR006463, MiaB_methiolase IPR007197, rSAM IPR023404, rSAM_horseshoe IPR002792, TRAM_dom
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF04055, Radical_SAM, 1 hit PF01938, TRAM, 1 hit PF00919, UPF0004, 1 hit
SFLDⁱ	SFLDF00273, (dimethylallyl)adenosine_tRNA, 1 hit SFLDS00029, Radical_SAM, 1 hit
SMARTⁱ	View protein in SMART SM00729, Elp3, 1 hit
TIGRFAMsⁱ	TIGR00089, TIGR00089, 1 hit
PROSITEⁱ	View protein in PROSITE PS51449, MTTASE_N, 1 hit PS01278, MTTASE_RADICAL, 1 hit PS51918, RADICAL_SAM, 1 hit PS50926, TRAM, 1 hit

Sequences (6+)ⁱ

Sequence statusⁱ: Complete.

Sequence processingⁱ: The displayed sequence is further processed into a mature form.

This entry describes 6 isoformsⁱ produced by alternative splicing. Align Add to basket

This entry has 6 described isoforms and 1 potential isoform that is computationally mapped.Show all Align All

Isoform 1 (identifier: Q96SZ6-1) [UniParc]FASTA Add to basket

This isoform has been chosen as the canonicalⁱ sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MHPLQCVLQV QRSLGWGPLA SVSWLSLRMC RAHSSLSSTM CPSPERQEDG 
        60         70         80         90        100
ARKDFSSRLA AGPTFQHFLK SASAPQEKLS SEVEDPPPYL MMDELLGRQR 
       110        120        130        140        150
KVYLETYGCQ MNVNDTEIAW SILQKSGYLR TSNLQEADVI LLVTCSIREK 
       160        170        180        190        200
AEQTIWNRLH QLKALKTRRP RSRVPLRIGI LGCMAERLKE EILNREKMVD 
       210        220        230        240        250
ILAGPDAYRD LPRLLAVAES GQQAANVLLS LDETYADVMP VQTSASATSA 
       260        270        280        290        300
FVSIMRGCDN MCSYCIVPFT RGRERSRPIA SILEEVKKLS EQVFLPPRPP 
       310        320        330        340        350
KVLGLQGLKE VTLLGQNVNS FRDNSEVQFN SAVPTNLSRG FTTNYKTKQG 
       360        370        380        390        400
GLRFAHLLDQ VSRVDPEMRI RFTSPHPKDF PDEVLQLIHE RDNICKQIHL 
       410        420        430        440        450
PAQSGSSRVL EAMRRGYSRE AYVELVHHIR ESIPGVSLSS DFIAGFCGET 
       460        470        480        490        500
EEDHVQTVSL LREVQYNMGF LFAYSMRQKT RAYHRLKDDV PEEVKLRRLE 
       510        520        530        540        550
ELITIFREEA TKANQTSVGC TQLVLVEGLS KRSATDLCGR NDGNLKVIFP 
       560        570        580        590        600
DAEMEDVNNP GLRVRAQPGD YVLVKITSAS SQTLRGHVLC RTTLRDSSAY 

C

Note: May be due to intron retention.

Length:601

Mass (Da):67,689

Last modified:June 16, 2003 - v2

Checksum:ⁱ4AEBFD7DA5400902

GO

Isoform 2 (identifier: Q96SZ6-2) [UniParc]FASTA Add to basket

The sequence of this isoform differs from the canonical sequence as follows:
1-90: Missing.
293-306: Missing.

« Hide

        10         20         30         40         50
MMDELLGRQR KVYLETYGCQ MNVNDTEIAW SILQKSGYLR TSNLQEADVI 
        60         70         80         90        100
LLVTCSIREK AEQTIWNRLH QLKALKTRRP RSRVPLRIGI LGCMAERLKE 
       110        120        130        140        150
EILNREKMVD ILAGPDAYRD LPRLLAVAES GQQAANVLLS LDETYADVMP 
       160        170        180        190        200
VQTSASATSA FVSIMRGCDN MCSYCIVPFT RGRERSRPIA SILEEVKKLS 
       210        220        230        240        250
EQGLKEVTLL GQNVNSFRDN SEVQFNSAVP TNLSRGFTTN YKTKQGGLRF 
       260        270        280        290        300
AHLLDQVSRV DPEMRIRFTS PHPKDFPDEV LQLIHERDNI CKQIHLPAQS 
       310        320        330        340        350
GSSRVLEAMR RGYSREAYVE LVHHIRESIP GVSLSSDFIA GFCGETEEDH 
       360        370        380        390        400
VQTVSLLREV QYNMGFLFAY SMRQKTRAYH RLKDDVPEEV KLRRLEELIT 
       410        420        430        440        450
IFREEATKAN QTSVGCTQLV LVEGLSKRSA TDLCGRNDGN LKVIFPDAEM 
       460        470        480        490 
EDVNNPGLRV RAQPGDYVLV KITSASSQTL RGHVLCRTTL RDSSAYC

Show »

Length:497

Mass (Da):56,223

Checksum:ⁱC8FFBA14A5C3EB09

GO

Isoform 3 (identifier: Q96SZ6-3) [UniParc]FASTA Add to basket

Also known as: CDK5RAP1_v11 Publication, isoform a

The sequence of this isoform differs from the canonical sequence as follows:
293-306: Missing.

« Hide

        10         20         30         40         50
MHPLQCVLQV QRSLGWGPLA SVSWLSLRMC RAHSSLSSTM CPSPERQEDG 
        60         70         80         90        100
ARKDFSSRLA AGPTFQHFLK SASAPQEKLS SEVEDPPPYL MMDELLGRQR 
       110        120        130        140        150
KVYLETYGCQ MNVNDTEIAW SILQKSGYLR TSNLQEADVI LLVTCSIREK 
       160        170        180        190        200
AEQTIWNRLH QLKALKTRRP RSRVPLRIGI LGCMAERLKE EILNREKMVD 
       210        220        230        240        250
ILAGPDAYRD LPRLLAVAES GQQAANVLLS LDETYADVMP VQTSASATSA 
       260        270        280        290        300
FVSIMRGCDN MCSYCIVPFT RGRERSRPIA SILEEVKKLS EQGLKEVTLL 
       310        320        330        340        350
GQNVNSFRDN SEVQFNSAVP TNLSRGFTTN YKTKQGGLRF AHLLDQVSRV 
       360        370        380        390        400
DPEMRIRFTS PHPKDFPDEV LQLIHERDNI CKQIHLPAQS GSSRVLEAMR 
       410        420        430        440        450
RGYSREAYVE LVHHIRESIP GVSLSSDFIA GFCGETEEDH VQTVSLLREV 
       460        470        480        490        500
QYNMGFLFAY SMRQKTRAYH RLKDDVPEEV KLRRLEELIT IFREEATKAN 
       510        520        530        540        550
QTSVGCTQLV LVEGLSKRSA TDLCGRNDGN LKVIFPDAEM EDVNNPGLRV 
       560        570        580 
RAQPGDYVLV KITSASSQTL RGHVLCRTTL RDSSAYC

Show »

Length:587

Mass (Da):66,146

Checksum:ⁱ314E826B35C346EB

GO

Isoform 4 (identifier: Q96SZ6-4) [UniParc]FASTA Add to basket

Also known as: isoform d

The sequence of this isoform differs from the canonical sequence as follows:
293-383: Missing.

« Hide

        10         20         30         40         50
MHPLQCVLQV QRSLGWGPLA SVSWLSLRMC RAHSSLSSTM CPSPERQEDG 
        60         70         80         90        100
ARKDFSSRLA AGPTFQHFLK SASAPQEKLS SEVEDPPPYL MMDELLGRQR 
       110        120        130        140        150
KVYLETYGCQ MNVNDTEIAW SILQKSGYLR TSNLQEADVI LLVTCSIREK 
       160        170        180        190        200
AEQTIWNRLH QLKALKTRRP RSRVPLRIGI LGCMAERLKE EILNREKMVD 
       210        220        230        240        250
ILAGPDAYRD LPRLLAVAES GQQAANVLLS LDETYADVMP VQTSASATSA 
       260        270        280        290        300
FVSIMRGCDN MCSYCIVPFT RGRERSRPIA SILEEVKKLS EQVLQLIHER 
       310        320        330        340        350
DNICKQIHLP AQSGSSRVLE AMRRGYSREA YVELVHHIRE SIPGVSLSSD 
       360        370        380        390        400
FIAGFCGETE EDHVQTVSLL REVQYNMGFL FAYSMRQKTR AYHRLKDDVP 
       410        420        430        440        450
EEVKLRRLEE LITIFREEAT KANQTSVGCT QLVLVEGLSK RSATDLCGRN 
       460        470        480        490        500
DGNLKVIFPD AEMEDVNNPG LRVRAQPGDY VLVKITSASS QTLRGHVLCR 
       510
TTLRDSSAYC

Show »

Length:510

Mass (Da):57,413

Checksum:ⁱ8F0DFB3B71E135BB

GO

Isoform 5 (identifier: Q96SZ6-5) [UniParc]FASTA Add to basket

Also known as: CDK5RAP1_v41 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     292-305: Missing.
     435-440: GVSLSS → EDTGIS
     441-601: Missing.

« Hide

        10         20         30         40         50
MHPLQCVLQV QRSLGWGPLA SVSWLSLRMC RAHSSLSSTM CPSPERQEDG 
        60         70         80         90        100
ARKDFSSRLA AGPTFQHFLK SASAPQEKLS SEVEDPPPYL MMDELLGRQR 
       110        120        130        140        150
KVYLETYGCQ MNVNDTEIAW SILQKSGYLR TSNLQEADVI LLVTCSIREK 
       160        170        180        190        200
AEQTIWNRLH QLKALKTRRP RSRVPLRIGI LGCMAERLKE EILNREKMVD 
       210        220        230        240        250
ILAGPDAYRD LPRLLAVAES GQQAANVLLS LDETYADVMP VQTSASATSA 
       260        270        280        290        300
FVSIMRGCDN MCSYCIVPFT RGRERSRPIA SILEEVKKLS EQGLKEVTLL 
       310        320        330        340        350
GQNVNSFRDN SEVQFNSAVP TNLSRGFTTN YKTKQGGLRF AHLLDQVSRV 
       360        370        380        390        400
DPEMRIRFTS PHPKDFPDEV LQLIHERDNI CKQIHLPAQS GSSRVLEAMR 
       410        420 
RGYSREAYVE LVHHIRESIP EDTGIS

Show »

Length:426

Mass (Da):48,072

Checksum:ⁱD74ADCD179EA4FDC

GO

Isoform 6 (identifier: Q96SZ6-6) [UniParc]FASTA Add to basket

Also known as: CDK5RAP1_v31 Publication

The sequence of this isoform differs from the canonical sequence as follows:
292-305: Missing.
576-601: ITSASSQTLRGHVLCRTTLRDSSAYC → VRSPFGLLACTVK

« Hide

        10         20         30         40         50
MHPLQCVLQV QRSLGWGPLA SVSWLSLRMC RAHSSLSSTM CPSPERQEDG 
        60         70         80         90        100
ARKDFSSRLA AGPTFQHFLK SASAPQEKLS SEVEDPPPYL MMDELLGRQR 
       110        120        130        140        150
KVYLETYGCQ MNVNDTEIAW SILQKSGYLR TSNLQEADVI LLVTCSIREK 
       160        170        180        190        200
AEQTIWNRLH QLKALKTRRP RSRVPLRIGI LGCMAERLKE EILNREKMVD 
       210        220        230        240        250
ILAGPDAYRD LPRLLAVAES GQQAANVLLS LDETYADVMP VQTSASATSA 
       260        270        280        290        300
FVSIMRGCDN MCSYCIVPFT RGRERSRPIA SILEEVKKLS EQGLKEVTLL 
       310        320        330        340        350
GQNVNSFRDN SEVQFNSAVP TNLSRGFTTN YKTKQGGLRF AHLLDQVSRV 
       360        370        380        390        400
DPEMRIRFTS PHPKDFPDEV LQLIHERDNI CKQIHLPAQS GSSRVLEAMR 
       410        420        430        440        450
RGYSREAYVE LVHHIRESIP GVSLSSDFIA GFCGETEEDH VQTVSLLREV 
       460        470        480        490        500
QYNMGFLFAY SMRQKTRAYH RLKDDVPEEV KLRRLEELIT IFREEATKAN 
       510        520        530        540        550
QTSVGCTQLV LVEGLSKRSA TDLCGRNDGN LKVIFPDAEM EDVNNPGLRV 
       560        570 
RAQPGDYVLV KVRSPFGLLA CTVK

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Length:574

Mass (Da):64,709

Checksum:ⁱA542DA7E2496A56B

GO

Computationally mapped potential isoform sequencesⁱ

There is 1 potential isoform mapped to this entry.BLAST Align Show all Add to basket

	Entry	Entry name		Protein names	Gene names	Length	Annotation

	H0Y721	H0Y721_HUMAN		Mitochondrial tRNA methylthiotransf... Mitochondrial tRNA methylthiotransferase CDK5RAP1	CDK5RAP1	256	Annotation score:

Sequence cautionⁱ

The sequence AAD34147 differs from that shown. Reason: Frameshift.Curated

The sequence AAF29131 differs from that shown. Reason: Frameshift.Curated

The sequence BAB55120 differs from that shown. Reason: Erroneous termination. Truncated C-terminus.Curated

Experimental Info

Feature key	Position(s)	DescriptionActions	Length
Sequence conflictⁱ	213	R → Q in AAH01215 (PubMed:15489334).Curated	1
Sequence conflictⁱ	217	V → D (PubMed:11042152).Curated	1
Sequence conflictⁱ	269	F → L in BAB55120 (PubMed:14702039).Curated	1
Sequence conflictⁱ	282	I → T in BAB55120 (PubMed:14702039).Curated	1
Sequence conflictⁱ	323	D → G in BAB55120 (PubMed:14702039).Curated	1
Sequence conflictⁱ	464	V → A in BAB14760 (PubMed:14702039).Curated	1
Sequence conflictⁱ	511	T → S in AAF29131 (PubMed:11042152).Curated	1
Sequence conflictⁱ	579	Missing (PubMed:10810093).Curated	1
Sequence conflictⁱ	585	R → K in BAB14760 (PubMed:14702039).Curated	1

Alternative sequence

Feature key	Position(s)	DescriptionActions	Length
Alternative sequenceⁱVSP_007560	1 – 90	Missing in isoform 2. 1 PublicationAdd BLAST	90
Alternative sequenceⁱVSP_047799	292 – 305	Missing in isoform 5 and isoform 6. 1 PublicationAdd BLAST	14
Alternative sequenceⁱVSP_007561	293 – 383	Missing in isoform 4. 1 PublicationAdd BLAST	91
Alternative sequenceⁱVSP_007562	293 – 306	Missing in isoform 2 and isoform 3. 2 PublicationsAdd BLAST	14
Alternative sequenceⁱVSP_047800	435 – 440	GVSLSS → EDTGIS in isoform 5. 1 Publication	6
Alternative sequenceⁱVSP_047801	441 – 601	Missing in isoform 5. 1 PublicationAdd BLAST	161
Alternative sequenceⁱVSP_047802	576 – 601	ITSAS…SSAYC → VRSPFGLLACTVK in isoform 6. 1 PublicationAdd BLAST	26

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	AF152097 mRNA Translation: AAD34147.1 Frameshift. AF161516 mRNA Translation: AAF29131.1 Frameshift. AY462283 mRNA Translation: AAS18317.1 AY462284 mRNA Translation: AAS18318.1 AK023992 mRNA Translation: BAB14760.1 AK027449 mRNA Translation: BAB55120.1 Sequence problems. AK292075 mRNA Translation: BAF84764.1 AL355392 Genomic DNA No translation available. CH471077 Genomic DNA Translation: EAW76319.1 CH471077 Genomic DNA Translation: EAW76322.1 CH471077 Genomic DNA Translation: EAW76323.1 BC001215 mRNA Translation: AAH01215.1 BC050706 mRNA Translation: AAH50706.1
The Consensus CDS (CCDS) project More...CCDSⁱ	CCDS13219.1 [Q96SZ6-3] CCDS63255.1 [Q96SZ6-4]
NCBI Reference Sequences More...RefSeqⁱ	NP_001265097.1, NM_001278168.1 [Q96SZ6-4] NP_001265098.1, NM_001278169.1 NP_057166.4, NM_016082.4 NP_057492.2, NM_016408.3 [Q96SZ6-3]

Genome annotation databases

Ensemblⁱ	ENST00000339269; ENSP00000341840; ENSG00000101391 [Q96SZ6-4] ENST00000346416; ENSP00000217372; ENSG00000101391 [Q96SZ6-3] ENST00000357886; ENSP00000350558; ENSG00000101391 [Q96SZ6-1] ENST00000473997; ENSP00000476857; ENSG00000101391 [Q96SZ6-2]
GeneIDⁱ	51654
KEGGⁱ	hsa:51654
UCSC genome browser More...UCSCⁱ	uc002wyz.5, human [Q96SZ6-1]

Keywords - Coding sequence diversityⁱ

Alternative splicing

Similar proteinsⁱ

100% Identity
90% Identity
50% Identity

Protein	Similar proteins		Species	Score	Length	Source
Q96SZ6-3	CDK5 regulatory subunit associated protein 1 isoform 2 (Fragment)		HUMAN		587	UniRef100_Q96SZ6-3
Q96SZ6-4	CDK5 regulatory subunit associated protein 1 isoform 1 (Fragment)		HUMAN		510	UniRef100_Q96SZ6-4

Protein	Similar proteins		Species	Score	Length	Source
Q96SZ6	Uncharacterized protein		PONAB		636	UniRef90_Q96SZ6
Uncharacterized protein		NOMLE		601
Uncharacterized protein		PAPAN		601
Uncharacterized protein		RHIRO		601
Uncharacterized protein		RHIBE		601
+112
Q96SZ6-5	MTTase N-terminal domain-containing protein (Fragment)		GULGU		417	UniRef90_Q96SZ6-5
MTTase N-terminal domain-containing protein		MANLE		348

Protein	Similar proteins		Species	Score	Length	Source
Q96SZ6	Uncharacterized protein		PONAB		636	UniRef50_Q96SZ6
Uncharacterized protein		PAPAN		601
Uncharacterized protein		NOMLE		601
Uncharacterized protein		RHIRO		601
Uncharacterized protein		RHIBE		601
+158
Q96SZ6-5	MTTase N-terminal domain-containing protein (Fragment)		GULGU		417	UniRef50_Q96SZ6-5
MTTase N-terminal domain-containing protein		MANLE		348
tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB (Fragment)		Porphyromonadaceae bacterium		391
CDK5RAP1-like protein		ZEUCU		441
tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase		Bacteroidetes bacterium HLUCCA01		438
+8

Cross-referencesⁱ

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	AF152097 mRNA Translation: AAD34147.1 Frameshift. AF161516 mRNA Translation: AAF29131.1 Frameshift. AY462283 mRNA Translation: AAS18317.1 AY462284 mRNA Translation: AAS18318.1 AK023992 mRNA Translation: BAB14760.1 AK027449 mRNA Translation: BAB55120.1 Sequence problems. AK292075 mRNA Translation: BAF84764.1 AL355392 Genomic DNA No translation available. CH471077 Genomic DNA Translation: EAW76319.1 CH471077 Genomic DNA Translation: EAW76322.1 CH471077 Genomic DNA Translation: EAW76323.1 BC001215 mRNA Translation: AAH01215.1 BC050706 mRNA Translation: AAH50706.1
CCDSⁱ	CCDS13219.1 [Q96SZ6-3] CCDS63255.1 [Q96SZ6-4]
RefSeqⁱ	NP_001265097.1, NM_001278168.1 [Q96SZ6-4] NP_001265098.1, NM_001278169.1 NP_057166.4, NM_016082.4 NP_057492.2, NM_016408.3 [Q96SZ6-3]

3D structure databases

ModBaseⁱ	Search...
SWISS-MODEL-Workspaceⁱ	Submit a new modelling project...

Protein-protein interaction databases

BioGRIDⁱ	119661, 63 interactors
IntActⁱ	Q96SZ6, 18 interactors
STRINGⁱ	9606.ENSP00000217372

PTM databases

iPTMnetⁱ	Q96SZ6
PhosphoSitePlusⁱ	Q96SZ6

Genetic variation databases

BioMutaⁱ	CDK5RAP1
DMDMⁱ	32129446

Proteomic databases

EPDⁱ	Q96SZ6
jPOSTⁱ	Q96SZ6
MassIVEⁱ	Q96SZ6
MaxQBⁱ	Q96SZ6
PaxDbⁱ	Q96SZ6
PeptideAtlasⁱ	Q96SZ6
PRIDEⁱ	Q96SZ6
ProteomicsDBⁱ	65981 78165 [Q96SZ6-1] 78166 [Q96SZ6-2] 78167 [Q96SZ6-3] 78168 [Q96SZ6-4]

Protocols and materials databases

Antibodypediaⁱ	43007, 171 antibodies
The DNASU plasmid repository More...DNASUⁱ	51654

Genome annotation databases

Ensemblⁱ	ENST00000339269; ENSP00000341840; ENSG00000101391 [Q96SZ6-4] ENST00000346416; ENSP00000217372; ENSG00000101391 [Q96SZ6-3] ENST00000357886; ENSP00000350558; ENSG00000101391 [Q96SZ6-1] ENST00000473997; ENSP00000476857; ENSG00000101391 [Q96SZ6-2]
GeneIDⁱ	51654
KEGGⁱ	hsa:51654
UCSCⁱ	uc002wyz.5, human [Q96SZ6-1]

Organism-specific databases

CTDⁱ	51654
DisGeNETⁱ	51654
GeneCardsⁱ	CDK5RAP1
HGNCⁱ	HGNC:15880, CDK5RAP1
HPAⁱ	ENSG00000101391, Low tissue specificity
MIMⁱ	608200, gene
neXtProtⁱ	NX_Q96SZ6
OpenTargetsⁱ	ENSG00000101391
PharmGKBⁱ	PA26313
VEuPathDBⁱ	HostDB:ENSG00000101391.20
GenAtlas: human gene database More...GenAtlasⁱ	Search...

Phylogenomic databases

eggNOGⁱ	KOG2492, Eukaryota
GeneTreeⁱ	ENSGT00940000160361
HOGENOMⁱ	CLU_018697_2_1_1
InParanoidⁱ	Q96SZ6
OMAⁱ	CEHFHIP
OrthoDBⁱ	835984at2759
PhylomeDBⁱ	Q96SZ6
TreeFamⁱ	TF101033

Enzyme and pathway databases

PathwayCommonsⁱ	Q96SZ6

PathwayCommonsⁱ

Q96SZ6

Miscellaneous databases

BioGRID-ORCSⁱ	51654, 5 hits in 994 CRISPR screens
ChiTaRSⁱ	CDK5RAP1, human
GeneWikiⁱ	CDK5RAP1
GenomeRNAiⁱ	51654
Pharosⁱ	Q96SZ6, Tbio
Protein Ontology More...PROⁱ	PR:Q96SZ6
RNActⁱ	Q96SZ6, protein
SOURCEⁱ	Search...

Gene expression databases

Bgeeⁱ	ENSG00000101391, Expressed in small intestine Peyer's patch and 238 other tissues
ExpressionAtlasⁱ	Q96SZ6, baseline and differential
Genevisibleⁱ	Q96SZ6, HS

Family and domain databases

Gene3Dⁱ	3.40.50.12160, 1 hit 3.80.30.20, 1 hit
HAMAPⁱ	MF_01864, tRNA_metthiotr_MiaB, 1 hit
InterProⁱ	View protein in InterPro IPR006638, Elp3/MiaB/NifB IPR005839, Methylthiotransferase IPR020612, Methylthiotransferase_CS IPR013848, Methylthiotransferase_N IPR038135, Methylthiotransferase_N_sf IPR006463, MiaB_methiolase IPR007197, rSAM IPR023404, rSAM_horseshoe IPR002792, TRAM_dom
Pfamⁱ	View protein in Pfam PF04055, Radical_SAM, 1 hit PF01938, TRAM, 1 hit PF00919, UPF0004, 1 hit
SFLDⁱ	SFLDF00273, (dimethylallyl)adenosine_tRNA, 1 hit SFLDS00029, Radical_SAM, 1 hit
SMARTⁱ	View protein in SMART SM00729, Elp3, 1 hit
TIGRFAMsⁱ	TIGR00089, TIGR00089, 1 hit
PROSITEⁱ	View protein in PROSITE PS51449, MTTASE_N, 1 hit PS01278, MTTASE_RADICAL, 1 hit PS51918, RADICAL_SAM, 1 hit PS50926, TRAM, 1 hit
ProtoNetⁱ	Search...
MobiDBⁱ	Search...

Entry informationⁱ

Entry nameⁱ	CK5P1_HUMAN
Accessionⁱ	Q96SZ6Primary (citable) accession number: Q96SZ6 Secondary accession number(s): A8K7R0 Q9Y3F0
Entry historyⁱ	Integrated into UniProtKB/Swiss-Prot:	June 16, 2003
	Last sequence update:	June 16, 2003
	Last modified:	April 7, 2021
	This is version 177 of the entry and version 2 of the sequence. See complete history.
Entry statusⁱ	Reviewed (UniProtKB/Swiss-Prot)
Annotation program	Chordata Protein Annotation Program
Disclaimer	Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousⁱ

Keywords - Technical termⁱ

Reference proteome

Documents

Human chromosome 20
Human chromosome 20: entries, gene names and cross-references to MIM
MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
SIMILARITY comments
Index of protein domains and families

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UniProtKB - Q96SZ6 (CK5P1_HUMAN)

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Mitochondrial tRNA methylthiotransferase CDK5RAP1

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<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Caution

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

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<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

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Keywords - Cellular componenti

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

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<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

GO - Molecular functioni

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<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

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<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Keywords - Domaini

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<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

Experimental Info

Alternative sequence

Sequence databases

Genome annotation databases

Keywords - Coding sequence diversityi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

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<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

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Functionⁱ

Catalytic activityⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

Keywords - Cellular componentⁱ

Pathology & Biotechⁱ

PTM / Processingⁱ

Expressionⁱ

Interactionⁱ

GO - Molecular functionⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Keywords - Domainⁱ

Sequence cautionⁱ

Keywords - Coding sequence diversityⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ

Keywords - Technical termⁱ