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Protein

Aminomethyltransferase, mitochondrial

Gene

AMT

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

The glycine cleavage system catalyzes the degradation of glycine.1 Publication

Catalytic activityi

[Protein]-S(8)-aminomethyldihydrolipoyllysine + tetrahydrofolate = [protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH3.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei232Substrate1 Publication1
Binding sitei261Substrate1 Publication1
Binding sitei399Substrate1 Publication1

GO - Molecular functioni

  • aminomethyltransferase activity Source: UniProtKB
  • transaminase activity Source: UniProtKB-KW

GO - Biological processi

  • glycine catabolic process Source: ProtInc
  • glycine decarboxylation via glycine cleavage system Source: UniProtKB
  • glyoxylate metabolic process Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Aminotransferase, Transferase

Enzyme and pathway databases

BioCyciMetaCyc:HS07223-MONOMER.
ZFISH:HS07223-MONOMER.
BRENDAi2.1.2.10. 2681.
ReactomeiR-HSA-6783984. Glycine degradation.
SABIO-RKP48728.

Names & Taxonomyi

Protein namesi
Recommended name:
Aminomethyltransferase, mitochondrialCurated (EC:2.1.2.101 Publication)
Alternative name(s):
Glycine cleavage system T protein1 Publication
Short name:
GCVT
Gene namesi
Name:AMTImported
Synonyms:GCST
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:473. AMT.

Subcellular locationi

  • Mitochondrion 1 Publication

GO - Cellular componenti

  • mitochondrial matrix Source: Reactome
  • mitochondrion Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Involvement in diseasei

Non-ketotic hyperglycinemia (NKH)6 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAutosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.
See also OMIM:605899
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00795142H → R in NKH. 1 PublicationCorresponds to variant rs121964983dbSNPEnsembl.1
Natural variantiVAR_00795247G → R in NKH. 1 PublicationCorresponds to variant rs121964982dbSNPEnsembl.1
Natural variantiVAR_016847145N → I in NKH; loss of aminomethyltransferase activity. 2 PublicationsCorresponds to variant rs386833682dbSNPEnsembl.1
Natural variantiVAR_016848211E → K in NKH. 1 PublicationCorresponds to variant rs116192290dbSNPEnsembl.1
Natural variantiVAR_074107265R → C in NKH. 1 PublicationCorresponds to variant rs779483959dbSNPEnsembl.1
Natural variantiVAR_007953269G → D in NKH; decreased aminomethyltransferase activity. 2 PublicationsCorresponds to variant rs121964981dbSNPEnsembl.1
Natural variantiVAR_007954276D → H in NKH. 1 PublicationCorresponds to variant rs121964984dbSNPEnsembl.1
Natural variantiVAR_007955320R → H in NKH; loss of aminomethyltransferase activity. 4 PublicationsCorresponds to variant rs121964985dbSNPEnsembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi129D → A or N: Loss of aminomethyltransferase activity. 1 Publication1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi275.
MalaCardsiAMT.
MIMi605899. phenotype.
OpenTargetsiENSG00000145020.
Orphaneti289863. Atypical glycine encephalopathy.
289860. Infantile glycine encephalopathy.
289857. Neonatal glycine encephalopathy.
PharmGKBiPA24780.

Chemistry databases

DrugBankiDB00116. Tetrahydrofolic acid.

Polymorphism and mutation databases

BioMutaiAMT.
DMDMi1346122.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 28MitochondrionBy similarityAdd BLAST28
ChainiPRO_000001075529 – 403Aminomethyltransferase, mitochondrialAdd BLAST375

Proteomic databases

EPDiP48728.
MaxQBiP48728.
PaxDbiP48728.
PeptideAtlasiP48728.
PRIDEiP48728.

PTM databases

iPTMnetiP48728.
PhosphoSitePlusiP48728.

Expressioni

Gene expression databases

BgeeiENSG00000145020.
CleanExiHS_AMT.
ExpressionAtlasiP48728. baseline and differential.
GenevisibleiP48728. HS.

Organism-specific databases

HPAiHPA005566.

Interactioni

Subunit structurei

The glycine cleavage system is composed of four proteins: P, T, L and H.1 Publication

Protein-protein interaction databases

BioGridi106772. 2 interactors.
IntActiP48728. 3 interactors.
STRINGi9606.ENSP00000273588.

Structurei

Secondary structure

1403
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi39 – 44Combined sources6
Beta strandi48 – 52Combined sources5
Beta strandi55 – 60Combined sources6
Helixi65 – 74Combined sources10
Beta strandi75 – 80Combined sources6
Beta strandi84 – 91Combined sources8
Helixi94 – 101Combined sources8
Beta strandi102 – 104Combined sources3
Beta strandi113 – 120Combined sources8
Beta strandi126 – 134Combined sources9
Beta strandi138 – 144Combined sources7
Helixi146 – 148Combined sources3
Helixi149 – 165Combined sources17
Beta strandi171 – 174Combined sources4
Beta strandi178 – 184Combined sources7
Helixi187 – 192Combined sources6
Helixi199 – 201Combined sources3
Beta strandi206 – 212Combined sources7
Beta strandi215 – 222Combined sources8
Beta strandi225 – 235Combined sources11
Helixi237 – 248Combined sources12
Beta strandi253 – 255Combined sources3
Helixi258 – 267Combined sources10
Turni273 – 275Combined sources3
Turni283 – 287Combined sources5
Helixi289 – 291Combined sources3
Helixi294 – 299Combined sources6
Helixi305 – 312Combined sources8
Beta strandi319 – 328Combined sources10
Beta strandi335 – 337Combined sources3
Beta strandi343 – 353Combined sources11
Turni354 – 357Combined sources4
Beta strandi358 – 365Combined sources8
Helixi367 – 369Combined sources3
Beta strandi375 – 380Combined sources6
Beta strandi383 – 390Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WSRX-ray2.00A/B29-403[»]
1WSVX-ray2.60A/B29-403[»]
ProteinModelPortaliP48728.
SMRiP48728.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP48728.

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvT family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG2770. Eukaryota.
COG0404. LUCA.
GeneTreeiENSGT00530000063120.
HOGENOMiHOG000239380.
HOVERGENiHBG005822.
InParanoidiP48728.
KOiK00605.
OMAiHSPILNM.
OrthoDBiEOG091G07Z1.
PhylomeDBiP48728.
TreeFamiTF313026.

Family and domain databases

Gene3Di2.40.30.110. 1 hit.
3.30.1360.120. 2 hits.
InterProiIPR006223. GCS_T.
IPR028896. GCST/DmdA.
IPR013977. GCV_T_C.
IPR006222. GCV_T_N.
IPR029043. GcvT/YgfZ_C.
IPR027266. TrmE/GcvT_dom1.
[Graphical view]
PfamiPF01571. GCV_T. 1 hit.
PF08669. GCV_T_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006487. GcvT. 1 hit.
SUPFAMiSSF101790. SSF101790. 1 hit.
TIGRFAMsiTIGR00528. gcvT. 1 hit.

Sequences (4)i

Sequence statusi: Complete.

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

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P48728-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' 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
MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV
60 70 80 90 100
AFAGWSLPVQ YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES
110 120 130 140 150
LVVGDIAELR PNQGTLSLFT NEAGGILDDL IVTNTSEGHL YVVSNAGCWE
160 170 180 190 200
KDLALMQDKV RELQNQGRDV GLEVLDNALL ALQGPTAAQV LQAGVADDLR
210 220 230 240 250
KLPFMTSAVM EVFGVSGCRV TRCGYTGEDG VEISVPVAGA VHLATAILKN
260 270 280 290 300
PEVKLAGLAA RDSLRLEAGL CLYGNDIDEH TTPVEGSLSW TLGKRRRAAM
310 320 330 340 350
DFPGAKVIVP QLKGRVQRRR VGLMCEGAPM RAHSPILNME GTKIGTVTSG
360 370 380 390 400
CPSPSLKKNV AMGYVPCEYS RPGTMLLVEV RRKQQMAVVS KMPFVPTNYY

TLK
Length:403
Mass (Da):43,946
Last modified:February 1, 1996 - v1
Checksum:i218DC9EEADFA9102
GO
Isoform 2 (identifier: P48728-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     30-85: Missing.

Note: No experimental confirmation available.
Show »
Length:347
Mass (Da):37,434
Checksum:i4C99E4B0F9C76299
GO
Isoform 3 (identifier: P48728-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     113-156: Missing.

Note: No experimental confirmation available.
Show »
Length:359
Mass (Da):39,267
Checksum:iB1DA25DDC565ECB8
GO
Isoform 4 (identifier: P48728-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     380-403: VRRKQQMAVVSKMPFVPTNYYTLK → LPSGPCF

Note: No experimental confirmation available.
Show »
Length:386
Mass (Da):41,780
Checksum:i3938EB3D01A8846B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti95V → C in BAA03512 (PubMed:8188235).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00795142H → R in NKH. 1 PublicationCorresponds to variant rs121964983dbSNPEnsembl.1
Natural variantiVAR_00795247G → R in NKH. 1 PublicationCorresponds to variant rs121964982dbSNPEnsembl.1
Natural variantiVAR_016847145N → I in NKH; loss of aminomethyltransferase activity. 2 PublicationsCorresponds to variant rs386833682dbSNPEnsembl.1
Natural variantiVAR_016848211E → K in NKH. 1 PublicationCorresponds to variant rs116192290dbSNPEnsembl.1
Natural variantiVAR_074107265R → C in NKH. 1 PublicationCorresponds to variant rs779483959dbSNPEnsembl.1
Natural variantiVAR_007953269G → D in NKH; decreased aminomethyltransferase activity. 2 PublicationsCorresponds to variant rs121964981dbSNPEnsembl.1
Natural variantiVAR_007954276D → H in NKH. 1 PublicationCorresponds to variant rs121964984dbSNPEnsembl.1
Natural variantiVAR_007955320R → H in NKH; loss of aminomethyltransferase activity. 4 PublicationsCorresponds to variant rs121964985dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_04255730 – 85Missing in isoform 2. 1 PublicationAdd BLAST56
Alternative sequenceiVSP_043288113 – 156Missing in isoform 3. 1 PublicationAdd BLAST44
Alternative sequenceiVSP_045418380 – 403VRRKQ…YYTLK → LPSGPCF in isoform 4. 1 PublicationAdd BLAST24

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13811 mRNA. Translation: BAA02967.1.
D14686 Genomic DNA. Translation: BAA03512.1.
AK290600 mRNA. Translation: BAF83289.1.
AK293481 mRNA. Translation: BAG56972.1.
AK296177 mRNA. Translation: BAG58912.1.
AC104452 Genomic DNA. No translation available.
CH471055 Genomic DNA. Translation: EAW64984.1.
BC007546 mRNA. Translation: AAH07546.2.
CCDSiCCDS2797.1. [P48728-1]
CCDS54583.1. [P48728-2]
CCDS54584.1. [P48728-3]
CCDS54585.1. [P48728-4]
PIRiI54192.
RefSeqiNP_000472.2. NM_000481.3. [P48728-1]
NP_001158182.1. NM_001164710.1. [P48728-3]
NP_001158183.1. NM_001164711.1. [P48728-2]
NP_001158184.1. NM_001164712.1. [P48728-4]
UniGeneiHs.102.

Genome annotation databases

EnsembliENST00000273588; ENSP00000273588; ENSG00000145020. [P48728-1]
ENST00000395338; ENSP00000378747; ENSG00000145020. [P48728-4]
ENST00000458307; ENSP00000415619; ENSG00000145020. [P48728-3]
ENST00000636522; ENSP00000489758; ENSG00000145020. [P48728-2]
GeneIDi275.
KEGGihsa:275.
UCSCiuc003cww.4. human. [P48728-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13811 mRNA. Translation: BAA02967.1.
D14686 Genomic DNA. Translation: BAA03512.1.
AK290600 mRNA. Translation: BAF83289.1.
AK293481 mRNA. Translation: BAG56972.1.
AK296177 mRNA. Translation: BAG58912.1.
AC104452 Genomic DNA. No translation available.
CH471055 Genomic DNA. Translation: EAW64984.1.
BC007546 mRNA. Translation: AAH07546.2.
CCDSiCCDS2797.1. [P48728-1]
CCDS54583.1. [P48728-2]
CCDS54584.1. [P48728-3]
CCDS54585.1. [P48728-4]
PIRiI54192.
RefSeqiNP_000472.2. NM_000481.3. [P48728-1]
NP_001158182.1. NM_001164710.1. [P48728-3]
NP_001158183.1. NM_001164711.1. [P48728-2]
NP_001158184.1. NM_001164712.1. [P48728-4]
UniGeneiHs.102.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WSRX-ray2.00A/B29-403[»]
1WSVX-ray2.60A/B29-403[»]
ProteinModelPortaliP48728.
SMRiP48728.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi106772. 2 interactors.
IntActiP48728. 3 interactors.
STRINGi9606.ENSP00000273588.

Chemistry databases

DrugBankiDB00116. Tetrahydrofolic acid.

PTM databases

iPTMnetiP48728.
PhosphoSitePlusiP48728.

Polymorphism and mutation databases

BioMutaiAMT.
DMDMi1346122.

Proteomic databases

EPDiP48728.
MaxQBiP48728.
PaxDbiP48728.
PeptideAtlasiP48728.
PRIDEiP48728.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000273588; ENSP00000273588; ENSG00000145020. [P48728-1]
ENST00000395338; ENSP00000378747; ENSG00000145020. [P48728-4]
ENST00000458307; ENSP00000415619; ENSG00000145020. [P48728-3]
ENST00000636522; ENSP00000489758; ENSG00000145020. [P48728-2]
GeneIDi275.
KEGGihsa:275.
UCSCiuc003cww.4. human. [P48728-1]

Organism-specific databases

CTDi275.
DisGeNETi275.
GeneCardsiAMT.
GeneReviewsiAMT.
HGNCiHGNC:473. AMT.
HPAiHPA005566.
MalaCardsiAMT.
MIMi238310. gene.
605899. phenotype.
neXtProtiNX_P48728.
OpenTargetsiENSG00000145020.
Orphaneti289863. Atypical glycine encephalopathy.
289860. Infantile glycine encephalopathy.
289857. Neonatal glycine encephalopathy.
PharmGKBiPA24780.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2770. Eukaryota.
COG0404. LUCA.
GeneTreeiENSGT00530000063120.
HOGENOMiHOG000239380.
HOVERGENiHBG005822.
InParanoidiP48728.
KOiK00605.
OMAiHSPILNM.
OrthoDBiEOG091G07Z1.
PhylomeDBiP48728.
TreeFamiTF313026.

Enzyme and pathway databases

BioCyciMetaCyc:HS07223-MONOMER.
ZFISH:HS07223-MONOMER.
BRENDAi2.1.2.10. 2681.
ReactomeiR-HSA-6783984. Glycine degradation.
SABIO-RKP48728.

Miscellaneous databases

ChiTaRSiAMT. human.
EvolutionaryTraceiP48728.
GenomeRNAii275.
PROiP48728.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000145020.
CleanExiHS_AMT.
ExpressionAtlasiP48728. baseline and differential.
GenevisibleiP48728. HS.

Family and domain databases

Gene3Di2.40.30.110. 1 hit.
3.30.1360.120. 2 hits.
InterProiIPR006223. GCS_T.
IPR028896. GCST/DmdA.
IPR013977. GCV_T_C.
IPR006222. GCV_T_N.
IPR029043. GcvT/YgfZ_C.
IPR027266. TrmE/GcvT_dom1.
[Graphical view]
PfamiPF01571. GCV_T. 1 hit.
PF08669. GCV_T_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006487. GcvT. 1 hit.
SUPFAMiSSF101790. SSF101790. 1 hit.
TIGRFAMsiTIGR00528. gcvT. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiGCST_HUMAN
AccessioniPrimary (citable) accession number: P48728
Secondary accession number(s): A8K3I5
, B4DE61, B4DJQ0, E9PBG1, Q96IG6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: November 30, 2016
This is version 159 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.