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UniProtKB - Q14004 (CDK13_HUMAN)

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Protein

Cyclin-dependent kinase 13

Gene

CDK13

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

Functioni

Cyclin-dependent kinase which displays CTD kinase activity and is required for RNA splicing. Has CTD kinase activity by hyperphosphorylating the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit RPB1, thereby acting as a key regulator of transcription elongation. Required for RNA splicing, probably by phosphorylating SRSF1/SF2. Required during hematopoiesis. In case of infection by HIV-1 virus, interacts with HIV-1 Tat protein acetylated at 'Lys-50' and 'Lys-51', thereby increasing HIV-1 mRNA splicing and promoting the production of the doubly spliced HIV-1 protein Nef.4 Publications

Catalytic activityi

ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate.1 Publication
ATP + a protein = ADP + a phosphoprotein.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei734ATPPROSITE-ProRule annotation1
Active sitei837Proton acceptorPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi711 – 719ATPPROSITE-ProRule annotation9

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

GO - Biological processi

  • alternative mRNA splicing, via spliceosome Source: UniProtKB
  • hemopoiesis Source: UniProtKB
  • multicellular organism development Source: ProtInc
  • negative regulation of stem cell differentiation Source: Ensembl
  • neutrophil degranulation Source: Reactome
  • phosphorylation of RNA polymerase II C-terminal domain Source: UniProtKB
  • positive regulation of cell proliferation Source: ProtInc
  • positive regulation of transcription by RNA polymerase II Source: GO_Central
  • regulation of mitotic nuclear division Source: ProtInc
  • transcription elongation from RNA polymerase II promoter Source: GO_Central
  • viral process Source: UniProtKB-KW
View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionKinase, Serine/threonine-protein kinase, Transferase
Biological processHost-virus interaction, mRNA processing, mRNA splicing
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-HSA-6798695 Neutrophil degranulation
SignaLinkiQ14004
SIGNORiQ14004

Names & Taxonomyi

Protein namesi
Recommended name:
Cyclin-dependent kinase 13 (EC:2.7.11.22, EC:2.7.11.23)
Alternative name(s):
CDC2-related protein kinase 5
Cell division cycle 2-like protein kinase 5
Cell division protein kinase 13
Short name:
hCDK13
Cholinesterase-related cell division controller
Gene namesi
Name:CDK13
Synonyms:CDC2L, CDC2L5, CHED, KIAA1791
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

EuPathDBiHostDB:ENSG00000065883.14
HGNCiHGNC:1733 CDK13
MIMi603309 gene
neXtProtiNX_Q14004

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (CHDFIDD)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal dominant syndrome characterized by atrial and/or ventricular septal congenital heart defects, facial dysmorphism with hypertelorism, upslanted palpebral fissures, epicanthal folds, ptosis, strabismus, posteriorly rotated ears, thin upper lip, and small mouth. Patients manifest global developmental delay, delayed walking and speech acquisition, and intellectual disability. Some patients have mild microcephaly, a small cerebral cortex, and agenesis of corpus callosum. More variable features include clinodactyly and/or camptodactyly of the fingers, hypotonia, and joint hypermobility.
See also OMIM:617360
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_078598714G → R in CHDFIDD. 1 PublicationCorresponds to variant dbSNP:rs1057519633Ensembl.1
Natural variantiVAR_078599717G → R in CHDFIDD. 1 PublicationCorresponds to variant dbSNP:rs1057519632Ensembl.1
Natural variantiVAR_079422734K → E in CHDFIDD. 1 PublicationCorresponds to variant dbSNP:rs1064795731Ensembl.1
Natural variantiVAR_078600751R → Q in CHDFIDD. 1 PublicationCorresponds to variant dbSNP:rs1057519634Ensembl.1
Natural variantiVAR_079423842N → D in CHDFIDD. 1 Publication1
Natural variantiVAR_078601842N → S in CHDFIDD. 2 PublicationsCorresponds to variant dbSNP:rs878853160EnsemblClinVar.1

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

DisGeNETi8621
MalaCardsiCDK13
MIMi617360 phenotype
OpenTargetsiENSG00000065883
PharmGKBiPA26264

Chemistry databases

ChEMBLiCHEMBL1795192
GuidetoPHARMACOLOGYi1966

Polymorphism and mutation databases

BioMutaiCDK13
DMDMi66774048

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000857111 – 1512Cyclin-dependent kinase 13Add BLAST1512

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei315PhosphoserineCombined sources1
Modified residuei317PhosphoserineCombined sources1
Modified residuei325PhosphoserineCombined sources1
Modified residuei340PhosphoserineCombined sources1
Modified residuei342PhosphoserineCombined sources1
Modified residuei358PhosphoserineCombined sources1
Modified residuei360PhosphoserineCombined sources1
Modified residuei383PhosphoserineCombined sources1
Modified residuei395PhosphoserineCombined sources1
Modified residuei397PhosphoserineCombined sources1
Modified residuei400PhosphoserineCombined sources1
Modified residuei437PhosphoserineCombined sources1
Modified residuei439PhosphoserineCombined sources1
Cross-linki519Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei525PhosphoserineCombined sources1
Cross-linki547Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei556N6-acetyllysineCombined sources1
Modified residuei588PhosphothreonineCombined sources1
Modified residuei871PhosphothreonineCombined sources1
Modified residuei1048PhosphoserineCombined sources1
Modified residuei1058PhosphothreonineBy similarity1
Modified residuei1246PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ14004
MaxQBiQ14004
PaxDbiQ14004
PeptideAtlasiQ14004
PRIDEiQ14004
ProteomicsDBi59786
59787 [Q14004-2]

PTM databases

iPTMnetiQ14004
PhosphoSitePlusiQ14004

Miscellaneous databases

PMAP-CutDBiQ14004

Expressioni

Tissue specificityi

Expressed in fetal brain, liver, muscle and in adult brain. Also expressed in neuroblastoma and glioblastoma tumors.

Gene expression databases

BgeeiENSG00000065883
CleanExiHS_CDC2L5
ExpressionAtlasiQ14004 baseline and differential
GenevisibleiQ14004 HS

Organism-specific databases

HPAiHPA059241

Interactioni

Subunit structurei

Interacts with CCNL1 and CCNL2 (By similarity). Interacts with CCNK. Interacts with C1QBP.By similarity2 Publications
(Microbial infection) Interacts with HIV-1 Tat.1 Publication

Binary interactionsi

Show more details

GO - Molecular functioni

  • cyclin binding Source: MGI
  • protein kinase binding Source: Ensembl
  • transcription factor binding Source: GO_Central
View the complete GO annotation on QuickGO ...

Protein-protein interaction databases

BioGridi114176, 65 interactors
ComplexPortaliCPX-359 Cyclin K-CDK13 complex
IntActiQ14004, 15 interactors
MINTiQ14004
STRINGi9606.ENSP00000181839

Chemistry databases

BindingDBiQ14004

Structurei

Secondary structure

11512
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi702 – 704Combined sources3
Beta strandi705 – 713Combined sources9
Beta strandi715 – 724Combined sources10
Turni725 – 727Combined sources3
Beta strandi730 – 736Combined sources7
Beta strandi739 – 741Combined sources3
Helixi747 – 758Combined sources12
Beta strandi767 – 772Combined sources6
Beta strandi787 – 792Combined sources6
Beta strandi795 – 797Combined sources3
Helixi798 – 804Combined sources7
Helixi811 – 830Combined sources20
Helixi840 – 842Combined sources3
Beta strandi843 – 845Combined sources3
Beta strandi851 – 853Combined sources3
Helixi856 – 858Combined sources3
Beta strandi864 – 866Combined sources3
Helixi877 – 879Combined sources3
Helixi882 – 885Combined sources4
Helixi894 – 908Combined sources15
Beta strandi909 – 911Combined sources3
Helixi919 – 930Combined sources12
Turni935 – 937Combined sources3
Helixi939 – 943Combined sources5
Turni945 – 950Combined sources6
Helixi960 – 963Combined sources4
Turni964 – 966Combined sources3
Helixi969 – 978Combined sources10
Turni983 – 985Combined sources3
Helixi989 – 994Combined sources6
Turni996 – 1000Combined sources5
Helixi1003 – 1005Combined sources3
Helixi1019 – 1024Combined sources6
Helixi1026 – 1030Combined sources5

3D structure databases

ProteinModelPortaliQ14004
SMRiQ14004
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini705 – 998Protein kinasePROSITE-ProRule annotationAdd BLAST294

Sequence similaritiesi

Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.Curated

Phylogenomic databases

eggNOGiKOG0600 Eukaryota
ENOG410XPIR LUCA
GeneTreeiENSGT00890000139396
HOVERGENiHBG050851
InParanoidiQ14004
KOiK08819
OMAiNVAPVKT
OrthoDBiEOG091G08Z8
PhylomeDBiQ14004
TreeFamiTF101060

Family and domain databases

InterProiView protein in InterPro
IPR011009 Kinase-like_dom_sf
IPR000719 Prot_kinase_dom
IPR017441 Protein_kinase_ATP_BS
IPR008271 Ser/Thr_kinase_AS
PfamiView protein in Pfam
PF00069 Pkinase, 1 hit
SMARTiView protein in SMART
SM00220 S_TKc, 1 hit
SUPFAMiSSF56112 SSF56112, 1 hit
PROSITEiView protein in PROSITE
PS00107 PROTEIN_KINASE_ATP, 1 hit
PS50011 PROTEIN_KINASE_DOM, 1 hit
PS00108 PROTEIN_KINASE_ST, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q14004-1) [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
MPSSSDTALG GGGGLSWAEK KLEERRKRRR FLSPQQPPLL LPLLQPQLLQ 
        60         70         80         90        100
PPPPPPPLLF LAAPGTAAAA AAAAAASSSC FSPGPPLEVK RLARGKRRAG 
       110        120        130        140        150
GRQKRRRGPR AGQEAEKRRV FSLPQPQQDG GGGASSGGGV TPLVEYEDVS 
       160        170        180        190        200
SQSEQGLLLG GASAATAATA AGGTGGSGGS PASSSGTQRR GEGSERRPRR 
       210        220        230        240        250
DRRSSSGRSK ERHREHRRRD GQRGGSEASK SRSRHSHSGE ERAEVAKSGS 
       260        270        280        290        300
SSSSGGRRKS ASATSSSSSS RKDRDSKAHR SRTKSSKEPP SAYKEPPKAY 
       310        320        330        340        350
REDKTEPKAY RRRRSLSPLG GRDDSPVSHR ASQSLRSRKS PSPAGGGSSP 
       360        370        380        390        400
YSRRLPRSPS PYSRRRSPSY SRHSSYERGG DVSPSPYSSS SWRRSRSPYS 
       410        420        430        440        450
PVLRRSGKSR SRSPYSSRHS RSRSRHRLSR SRSRHSSISP STLTLKSSLA 
       460        470        480        490        500
AELNKNKKAR AAEAARAAEA AKAAEATKAA EAAAKAAKAS NTSTPTKGNT 
       510        520        530        540        550
ETSASASQTN HVKDVKKIKI EHAPSPSSGG TLKNDKAKTK PPLQVTKVEN 
       560        570        580        590        600
NLIVDKATKK AVIVGKESKS AATKEESVSL KEKTKPLTPS IGAKEKEQHV 
       610        620        630        640        650
ALVTSTLPPL PLPPMLPEDK EADSLRGNIS VKAVKKEVEK KLRCLLADLP 
       660        670        680        690        700
LPPELPGGDD LSKSPEEKKT ATQLHSKRRP KICGPRYGET KEKDIDWGKR 
       710        720        730        740        750
CVDKFDIIGI IGEGTYGQVY KARDKDTGEM VALKKVRLDN EKEGFPITAI 
       760        770        780        790        800
REIKILRQLT HQSIINMKEI VTDKEDALDF KKDKGAFYLV FEYMDHDLMG 
       810        820        830        840        850
LLESGLVHFN ENHIKSFMRQ LMEGLDYCHK KNFLHRDIKC SNILLNNRGQ 
       860        870        880        890        900
IKLADFGLAR LYSSEESRPY TNKVITLWYR PPELLLGEER YTPAIDVWSC 
       910        920        930        940        950
GCILGELFTK KPIFQANQEL AQLELISRIC GSPCPAVWPD VIKLPYFNTM 
       960        970        980        990       1000
KPKKQYRRKL REEFVFIPAA ALDLFDYMLA LDPSKRCTAE QALQCEFLRD 
      1010       1020       1030       1040       1050
VEPSKMPPPD LPLWQDCHEL WSKKRRRQKQ MGMTDDVSTI KAPRKDLSLG 
      1060       1070       1080       1090       1100
LDDSRTNTPQ GVLPSSQLKS QGSSNVAPVK TGPGQHLNHS ELAILLNLLQ 
      1110       1120       1130       1140       1150
SKTSVNMADF VQVLNIKVNS ETQQQLNKIN LPAGILATGE KQTDPSTPQQ 
      1160       1170       1180       1190       1200
ESSKPLGGIQ PSSQTIQPKV ETDAAQAAVQ SAFAVLLTQL IKAQQSKQKD 
      1210       1220       1230       1240       1250
VLLEERENGS GHEASLQLRP PPEPSTPVSG QDDLIQHQDM RILELTPEPD 
      1260       1270       1280       1290       1300
RPRILPPDQR PPEPPEPPPV TEEDLDYRTE NQHVPTTSSS LTDPHAGVKA 
      1310       1320       1330       1340       1350
ALLQLLAQHQ PQDDPKREGG IDYQAGDTYV STSDYKDNFG SSSFSSAPYV 
      1360       1370       1380       1390       1400
SNDGLGSSSA PPLERRSFIG NSDIQSLDNY STASSHSGGP PQPSAFSESF 
      1410       1420       1430       1440       1450
PSSVAGYGDI YLNAGPMLFS GDKDHRFEYS HGPIAVLANS SDPSTGPEST 
      1460       1470       1480       1490       1500
HPLPAKMHNY NYGGNLQENP SGPSLMHGQT WTSPAQGPGY SQGYRGHIST 
      1510 
STGRGRGRGL PY
Length:1,512
Mass (Da):164,923
Last modified:May 10, 2005 - v2
Checksum:i3CA54A3585A2943D
GO
Isoform 2 (identifier: Q14004-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1079-1138: Missing.

Show »
Length:1,452
Mass (Da):158,435
Checksum:i8A8B712D8621EEA3
GO

Sequence cautioni

The sequence AAA58424 differs from that shown. Reason: Frameshift at position 1006.Curated
The sequence AAS07490 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti21K → R in CAC10400 (PubMed:11162436).Curated1
Sequence conflicti21K → R in CAC10401 (PubMed:11162436).Curated1
Sequence conflicti671A → T in CAC10400 (PubMed:11162436).Curated1
Sequence conflicti671A → T in CAC10401 (PubMed:11162436).Curated1
Sequence conflicti671A → T in AAA58424 (PubMed:1731328).Curated1
Sequence conflicti810N → Y in AAA58424 (PubMed:1731328).Curated1
Sequence conflicti862 – 866YSSEE → FSVFF in BAB47420 (Ref. 5) Curated5
Sequence conflicti1180Q → R in BAD96773 (Ref. 5) Curated1
Sequence conflicti1356G → E in BAD96773 (Ref. 5) Curated1

RNA editingi

Edited at position 103.1 Publication
Edited at about 88%.

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_066526103Q → R in RNA edited version. 1
Natural variantiVAR_053926340S → F. Corresponds to variant dbSNP:rs13622Ensembl.1
Natural variantiVAR_022381356P → A1 PublicationCorresponds to variant dbSNP:rs17537669EnsemblClinVar.1
Natural variantiVAR_022382403L → F1 PublicationCorresponds to variant dbSNP:rs3735137Ensembl.1
Natural variantiVAR_022383410R → Q1 PublicationCorresponds to variant dbSNP:rs17496261Ensembl.1
Natural variantiVAR_041965494T → A1 PublicationCorresponds to variant dbSNP:rs34624759Ensembl.1
Natural variantiVAR_022384500T → A2 PublicationsCorresponds to variant dbSNP:rs3735135Ensembl.1
Natural variantiVAR_022385624S → G1 PublicationCorresponds to variant dbSNP:rs17496275Ensembl.1
Natural variantiVAR_041966670T → R1 PublicationCorresponds to variant dbSNP:rs34775357Ensembl.1
Natural variantiVAR_022386700R → L2 PublicationsCorresponds to variant dbSNP:rs1057000Ensembl.1
Natural variantiVAR_078598714G → R in CHDFIDD. 1 PublicationCorresponds to variant dbSNP:rs1057519633Ensembl.1
Natural variantiVAR_078599717G → R in CHDFIDD. 1 PublicationCorresponds to variant dbSNP:rs1057519632Ensembl.1
Natural variantiVAR_079422734K → E in CHDFIDD. 1 PublicationCorresponds to variant dbSNP:rs1064795731Ensembl.1
Natural variantiVAR_078600751R → Q in CHDFIDD. 1 PublicationCorresponds to variant dbSNP:rs1057519634Ensembl.1
Natural variantiVAR_079423842N → D in CHDFIDD. 1 Publication1
Natural variantiVAR_078601842N → S in CHDFIDD. 2 PublicationsCorresponds to variant dbSNP:rs878853160EnsemblClinVar.1
Natural variantiVAR_0223871062V → M1 PublicationCorresponds to variant dbSNP:rs17496712Ensembl.1
Natural variantiVAR_0419671170V → M2 PublicationsCorresponds to variant dbSNP:rs3204309Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0135791079 – 1138Missing in isoform 2. 2 PublicationsAdd BLAST60

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ297709 mRNA Translation: CAC10400.1
AJ297710 mRNA Translation: CAC10401.1
AY679523 Genomic DNA Translation: AAT74623.1
AC072061 Genomic DNA Translation: AAS07490.1 Sequence problems.
AC072061 Genomic DNA Translation: AAS07491.1
AC006023 Genomic DNA Translation: AAD54514.1
M80629 mRNA Translation: AAA58424.1 Frameshift.
AK223053 mRNA Translation: BAD96773.1
AB058694 mRNA Translation: BAB47420.1
CCDSiCCDS5461.1 [Q14004-1]
CCDS5462.1 [Q14004-2]
PIRiA38197
RefSeqiNP_003709.3, NM_003718.4 [Q14004-1]
NP_112557.2, NM_031267.3 [Q14004-2]
UniGeneiHs.233552

Genome annotation databases

EnsembliENST00000181839; ENSP00000181839; ENSG00000065883 [Q14004-1]
ENST00000340829; ENSP00000340557; ENSG00000065883 [Q14004-2]
GeneIDi8621
KEGGihsa:8621
UCSCiuc003thh.5 human [Q14004-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism, RNA editing

Similar proteinsi

Entry informationi

Entry nameiCDK13_HUMAN
AccessioniPrimary (citable) accession number: Q14004
Secondary accession number(s): Q53G78
, Q6DKQ9, Q75MH4, Q75MH5, Q96JN4, Q9H4A0, Q9H4A1, Q9UDR4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: May 10, 2005
Last modified: July 18, 2018
This is version 183 of the entry and version 2 of the sequence. See 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 7
    Human chromosome 7: 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. Human and mouse protein kinases
    Human and mouse protein kinases: classification and index
  7. SIMILARITY comments
    Index of protein domains and families

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