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Protein

Pyridoxal-dependent decarboxylase domain-containing protein 1

Gene

PDXDC1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Cofactori

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Ligandi

Pyridoxal phosphate

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal-dependent decarboxylase domain-containing protein 1 (EC:4.1.1.-)
Gene namesi
Name:PDXDC1
Synonyms:KIAA0251
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:28995. PDXDC1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Organism-specific databases

DisGeNETi23042.
OpenTargetsiENSG00000179889.
ENSG00000275498.
ENSG00000276709.
PharmGKBiPA162399182.

Polymorphism and mutation databases

BioMutaiPDXDC1.
DMDMi156633546.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002976771 – 788Pyridoxal-dependent decarboxylase domain-containing protein 1Add BLAST788

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei414PhosphothreonineCombined sources1
Modified residuei652PhosphoserineCombined sources1
Modified residuei687PhosphothreonineBy similarity1
Modified residuei691PhosphothreonineCombined sources1
Modified residuei710PhosphoserineCombined sources1
Modified residuei718PhosphoserineCombined sources1
Modified residuei722PhosphoserineCombined sources1
Modified residuei748PhosphoserineBy similarity1
Modified residuei757PhosphoserineCombined sources1
Modified residuei779PhosphoserineCombined sources1
Modified residuei786PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ6P996.
MaxQBiQ6P996.
PaxDbiQ6P996.
PeptideAtlasiQ6P996.
PRIDEiQ6P996.

PTM databases

iPTMnetiQ6P996.
PhosphoSitePlusiQ6P996.

Expressioni

Gene expression databases

BgeeiENSG00000179889.
CleanExiHS_PDXDC1.
ExpressionAtlasiQ6P996. baseline and differential.
GenevisibleiQ6P996. HS.

Organism-specific databases

HPAiHPA047369.
HPA049121.
HPA051484.

Interactioni

GO - Molecular functioni

  • cadherin binding involved in cell-cell adhesion Source: BHF-UCL

Protein-protein interaction databases

BioGridi116681. 39 interactors.
IntActiQ6P996. 12 interactors.
MINTiMINT-5003736.
STRINGi9606.ENSP00000379691.

Structurei

3D structure databases

ProteinModelPortaliQ6P996.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the group II decarboxylase family.Curated

Phylogenomic databases

eggNOGiKOG0630. Eukaryota.
ENOG410XYFU. LUCA.
GeneTreeiENSGT00390000009628.
HOGENOMiHOG000115485.
HOVERGENiHBG069100.
InParanoidiQ6P996.
OMAiLVANAXV.
PhylomeDBiQ6P996.
TreeFamiTF313101.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR002129. PyrdxlP-dep_de-COase.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00282. Pyridoxal_deC. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 2 hits.

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q6P996-1) [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
MDASLEKIAD PTLAEMGKNL KEAVKMLEDS QRRTEEENGK KLISGDIPGP
60 70 80 90 100
LQGSGQDMVS ILQLVQNLMH GDEDEEPQSP RIQNIGEQGH MALLGHSLGA
110 120 130 140 150
YISTLDKEKL RKLTTRILSD TTLWLCRIFR YENGCAYFHE EEREGLAKIC
160 170 180 190 200
RLAIHSRYED FVVDGFNVLY NKKPVIYLSA AARPGLGQYL CNQLGLPFPC
210 220 230 240 250
LCRVPCNTVF GSQHQMDVAF LEKLIKDDIE RGRLPLLLVA NAGTAAVGHT
260 270 280 290 300
DKIGRLKELC EQYGIWLHVE GVNLATLALG YVSSSVLAAA KCDSMTMTPG
310 320 330 340 350
PWLGLPAVPA VTLYKHDDPA LTLVAGLTSN KPTDKLRALP LWLSLQYLGL
360 370 380 390 400
DGFVERIKHA CQLSQRLQES LKKVNYIKIL VEDELSSPVV VFRFFQELPG
410 420 430 440 450
SDPVFKAVPV PNMTPSGVGR ERHSCDALNR WLGEQLKQLV PASGLTVMDL
460 470 480 490 500
EAEGTCLRFS PLMTAAVLGT RGEDVDQLVA CIESKLPVLC CTLQLREEFK
510 520 530 540 550
QEVEATAGLL YVDDPNWSGI GVVRYEHAND DKSSLKSDPE GENIHAGLLK
560 570 580 590 600
KLNELESDLT FKIGPEYKSM KSCLYVGMAS DNVDAAELVE TIAATAREIE
610 620 630 640 650
ENSRLLENMT EVVRKGIQEA QVELQKASEE RLLEEGVLRQ IPVVGSVLNW
660 670 680 690 700
FSPVQALQKG RTFNLTAGSL ESTEPIYVYK AQGAGVTLPP TPSGSRTKQR
710 720 730 740 750
LPGQKPFKRS LRGSDALSET SSVSHIEDLE KVERLSSGPE QITLEASSTE
760 770 780
GHPGAPSPQH TDQTEAFQKG VPHPEDDHSQ VEGPESLR
Length:788
Mass (Da):86,707
Last modified:August 21, 2007 - v2
Checksum:i2BAFEDC0A1C13AD3
GO
Isoform 2 (identifier: Q6P996-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     194-216: Missing.
     432-452: LGEQLKQLVPASGLTVMDLEA → VRMAVTPLSFQVPVHHHPTCW
     453-788: Missing.

Show »
Length:429
Mass (Da):47,730
Checksum:iA2FFFC3D24DEAFFD
GO
Isoform 3 (identifier: Q6P996-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-15: Missing.
     54-129: Missing.

Show »
Length:697
Mass (Da):76,547
Checksum:i87825F4250E68775
GO
Isoform 4 (identifier: Q6P996-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     32-32: Missing.
     54-80: Missing.

Show »
Length:760
Mass (Da):83,571
Checksum:i6127FC4820F4F1B3
GO
Isoform 5 (identifier: Q6P996-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     54-80: Missing.

Show »
Length:761
Mass (Da):83,728
Checksum:i2D97292195CDE8DE
GO

Sequence cautioni

The sequence AAH33748 differs from that shown. Reason: Frameshift at position 369.Curated
The sequence AAZ14099 differs from that shown. Reason: Frameshift at position 369.Curated
The sequence BAA19780 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti37E → G in BAG61167 (PubMed:14702039).Curated1
Sequence conflicti53G → V in AAZ14099 (Ref. 5) Curated1
Sequence conflicti82I → M in BAG61167 (PubMed:14702039).Curated1
Sequence conflicti82I → M in AAZ14099 (Ref. 5) Curated1
Sequence conflicti114T → A in AAZ14099 (Ref. 5) Curated1
Sequence conflicti178L → F in AAZ14099 (Ref. 5) Curated1
Sequence conflicti373K → E in AAH60871 (PubMed:15489334).Curated1
Sequence conflicti749T → A in BAG61675 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_059252301P → L.1 PublicationCorresponds to variant rs4985162dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0557311 – 15Missing in isoform 3. 1 PublicationAdd BLAST15
Alternative sequenceiVSP_05573232Missing in isoform 4. 1 Publication1
Alternative sequenceiVSP_05573354 – 129Missing in isoform 3. 1 PublicationAdd BLAST76
Alternative sequenceiVSP_05573454 – 80Missing in isoform 4 and isoform 5. 1 PublicationAdd BLAST27
Alternative sequenceiVSP_027341194 – 216Missing in isoform 2. 1 PublicationAdd BLAST23
Alternative sequenceiVSP_027342432 – 452LGEQL…MDLEA → VRMAVTPLSFQVPVHHHPTC W in isoform 2. 1 PublicationAdd BLAST21
Alternative sequenceiVSP_027343453 – 788Missing in isoform 2. 1 PublicationAdd BLAST336

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D87438 mRNA. Translation: BAA19780.1. Different initiation.
AK299799 mRNA. Translation: BAG61675.1.
AK299111 mRNA. Translation: BAG61167.1.
AC138932 Genomic DNA. No translation available.
AC139256 Genomic DNA. No translation available.
BC025366 mRNA. Translation: AAH25366.2.
BC033748 mRNA. Translation: AAH33748.1. Frameshift.
BC036520 mRNA. Translation: AAH36520.1.
BC042104 mRNA. Translation: AAH42104.2.
BC060871 mRNA. Translation: AAH60871.1.
DQ111782 mRNA. Translation: AAZ14099.1. Frameshift.
CCDSiCCDS32393.1. [Q6P996-1]
CCDS66954.1. [Q6P996-5]
CCDS66955.1. [Q6P996-4]
CCDS66957.1. [Q6P996-3]
CCDS73831.1. [Q6P996-2]
RefSeqiNP_001272373.1. NM_001285444.1. [Q6P996-5]
NP_001272374.1. NM_001285445.1. [Q6P996-4]
NP_001272376.1. NM_001285447.1.
NP_001272377.1. NM_001285448.1. [Q6P996-3]
NP_001272379.1. NM_001285450.1. [Q6P996-2]
NP_055842.2. NM_015027.3. [Q6P996-1]
XP_006725288.1. XM_006725225.1. [Q6P996-1]
XP_006725291.1. XM_006725228.2. [Q6P996-5]
XP_006726660.1. XM_006726597.1. [Q6P996-1]
XP_006726663.1. XM_006726600.2. [Q6P996-5]
UniGeneiHs.370781.

Genome annotation databases

EnsembliENST00000396410; ENSP00000379691; ENSG00000179889. [Q6P996-1]
ENST00000450288; ENSP00000391147; ENSG00000179889. [Q6P996-3]
ENST00000455313; ENSP00000406703; ENSG00000179889. [Q6P996-2]
ENST00000569715; ENSP00000455070; ENSG00000179889. [Q6P996-5]
ENST00000613798; ENSP00000481784; ENSG00000275498. [Q6P996-2]
ENST00000614573; ENSP00000479054; ENSG00000276709. [Q6P996-2]
ENST00000614833; ENSP00000480418; ENSG00000275498. [Q6P996-3]
ENST00000618389; ENSP00000484595; ENSG00000275498. [Q6P996-1]
ENST00000619589; ENSP00000478686; ENSG00000275498. [Q6P996-5]
ENST00000627450; ENSP00000486662; ENSG00000179889. [Q6P996-4]
ENST00000631842; ENSP00000488664; ENSG00000275498. [Q6P996-4]
GeneIDi102724985.
23042.
KEGGihsa:102724985.
hsa:23042.
UCSCiuc002dcz.5. human. [Q6P996-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D87438 mRNA. Translation: BAA19780.1. Different initiation.
AK299799 mRNA. Translation: BAG61675.1.
AK299111 mRNA. Translation: BAG61167.1.
AC138932 Genomic DNA. No translation available.
AC139256 Genomic DNA. No translation available.
BC025366 mRNA. Translation: AAH25366.2.
BC033748 mRNA. Translation: AAH33748.1. Frameshift.
BC036520 mRNA. Translation: AAH36520.1.
BC042104 mRNA. Translation: AAH42104.2.
BC060871 mRNA. Translation: AAH60871.1.
DQ111782 mRNA. Translation: AAZ14099.1. Frameshift.
CCDSiCCDS32393.1. [Q6P996-1]
CCDS66954.1. [Q6P996-5]
CCDS66955.1. [Q6P996-4]
CCDS66957.1. [Q6P996-3]
CCDS73831.1. [Q6P996-2]
RefSeqiNP_001272373.1. NM_001285444.1. [Q6P996-5]
NP_001272374.1. NM_001285445.1. [Q6P996-4]
NP_001272376.1. NM_001285447.1.
NP_001272377.1. NM_001285448.1. [Q6P996-3]
NP_001272379.1. NM_001285450.1. [Q6P996-2]
NP_055842.2. NM_015027.3. [Q6P996-1]
XP_006725288.1. XM_006725225.1. [Q6P996-1]
XP_006725291.1. XM_006725228.2. [Q6P996-5]
XP_006726660.1. XM_006726597.1. [Q6P996-1]
XP_006726663.1. XM_006726600.2. [Q6P996-5]
UniGeneiHs.370781.

3D structure databases

ProteinModelPortaliQ6P996.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116681. 39 interactors.
IntActiQ6P996. 12 interactors.
MINTiMINT-5003736.
STRINGi9606.ENSP00000379691.

PTM databases

iPTMnetiQ6P996.
PhosphoSitePlusiQ6P996.

Polymorphism and mutation databases

BioMutaiPDXDC1.
DMDMi156633546.

Proteomic databases

EPDiQ6P996.
MaxQBiQ6P996.
PaxDbiQ6P996.
PeptideAtlasiQ6P996.
PRIDEiQ6P996.

Protocols and materials databases

DNASUi23042.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000396410; ENSP00000379691; ENSG00000179889. [Q6P996-1]
ENST00000450288; ENSP00000391147; ENSG00000179889. [Q6P996-3]
ENST00000455313; ENSP00000406703; ENSG00000179889. [Q6P996-2]
ENST00000569715; ENSP00000455070; ENSG00000179889. [Q6P996-5]
ENST00000613798; ENSP00000481784; ENSG00000275498. [Q6P996-2]
ENST00000614573; ENSP00000479054; ENSG00000276709. [Q6P996-2]
ENST00000614833; ENSP00000480418; ENSG00000275498. [Q6P996-3]
ENST00000618389; ENSP00000484595; ENSG00000275498. [Q6P996-1]
ENST00000619589; ENSP00000478686; ENSG00000275498. [Q6P996-5]
ENST00000627450; ENSP00000486662; ENSG00000179889. [Q6P996-4]
ENST00000631842; ENSP00000488664; ENSG00000275498. [Q6P996-4]
GeneIDi102724985.
23042.
KEGGihsa:102724985.
hsa:23042.
UCSCiuc002dcz.5. human. [Q6P996-1]

Organism-specific databases

CTDi23042.
DisGeNETi23042.
GeneCardsiPDXDC1.
H-InvDBHIX0013196.
HIX0019757.
HIX0173252.
HGNCiHGNC:28995. PDXDC1.
HPAiHPA047369.
HPA049121.
HPA051484.
MIMi614244. gene.
neXtProtiNX_Q6P996.
OpenTargetsiENSG00000179889.
ENSG00000275498.
ENSG00000276709.
PharmGKBiPA162399182.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0630. Eukaryota.
ENOG410XYFU. LUCA.
GeneTreeiENSGT00390000009628.
HOGENOMiHOG000115485.
HOVERGENiHBG069100.
InParanoidiQ6P996.
OMAiLVANAXV.
PhylomeDBiQ6P996.
TreeFamiTF313101.

Miscellaneous databases

ChiTaRSiPDXDC1. human.
PROiQ6P996.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000179889.
CleanExiHS_PDXDC1.
ExpressionAtlasiQ6P996. baseline and differential.
GenevisibleiQ6P996. HS.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR002129. PyrdxlP-dep_de-COase.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00282. Pyridoxal_deC. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 2 hits.
ProtoNetiSearch...

Entry informationi

Entry nameiPDXD1_HUMAN
AccessioniPrimary (citable) accession number: Q6P996
Secondary accession number(s): B4DR55
, B4DSL3, E7EMH5, E7EPL4, H3BNZ1, O00236, Q4F6X7, Q6PID7, Q86YF1, Q8N4Q9, Q8TBS5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 21, 2007
Last sequence update: August 21, 2007
Last modified: November 2, 2016
This is version 120 of the entry and version 2 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: 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. 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.