UROD uroporphyrinogen decarboxylase [Homo sapiens (human)] - Gene

Summary

Official Symbol: URODprovided by HGNC
Official Full Name: uroporphyrinogen decarboxylaseprovided by HGNC
Primary source: HGNC:HGNC:12591
See related: Ensembl:ENSG00000126088 MIM:613521
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PCT; UPD
Summary: This gene encodes an enzyme in the heme biosynthetic pathway. This enzyme is responsible for catalyzing the conversion of uroporphyrinogen to coproporphyrinogen through the removal of four carboxymethyl side chains. Mutations and deficiency in this enzyme are known to cause familial porphyria cutanea tarda and hepatoerythropoetic porphyria.[provided by RefSeq, Aug 2010]
Expression: Ubiquitous expression in bone marrow (RPKM 73.9), adrenal (RPKM 43.0) and 25 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 1p34.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
109	current	GRCh38.p12 (GCF_000001405.38)	1	NC_000001.11 (45012133..45015669)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (45477805..45481341)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

a new mutation in the UROD gene in Egyptian patients with Hepatoerythropoietic porphyria, is reported.
Title: Hepatoerythropoietic Porphyria Caused by a Novel Homoallelic Mutation in Uroporphyrinogen Decarboxylase Gene in Egyptian Patients.
a new insight in the conformational changes occurred in the mutant structures of UROD protein.
Title: Computational identification of pathogenic associated nsSNPs and its structural impact in UROD gene: a molecular dynamics approach.
Data suggest that the traditional Chinese medicine (TCM) candidate potential three-in-one inhibitors for three drug target proteins epidermal growth factor receptor (EGFR), Her2, and uroporphyrinogen decarboxylase (UROD) against head and neck cancer.
Title: A possible strategy against head and neck cancer: in silico investigation of three-in-one inhibitors.
Expression of the D306Y mutation results in an insoluble recombinant protein. G318R and K297N have little effect on the structure or activity of recombinant URO-D, but the proteins display reduced stability in vitro.
Title: Structural and kinetic characterization of mutant human uroporphyrinogen decarboxylases.
Among seventeen F-PCT patients, sixteen UROD mutations were identified.
Title: Familial porphyria cutanea tarda in Spain: characterization of eight novel mutations in the UROD gene and haplotype analysis of the common p.G281E mutation.
analysis of uroporphyrinogen decarboxylase as a potential target for specific components of traditional Chinese medicine
Title: Uroporphyrinogen decarboxylase as a potential target for specific components of traditional Chinese medicine: a virtual screening and molecular dynamics study.
Mutations in UROD gene is associated with familial porphyria cutanea tarda.
Title: Molecular analysis of the UROD gene in 17 Argentinean patients with familial porphyria cutanea tarda: characterization of four novel mutations.
Hepatoerythropoietic porphyria and familial porphyria cutanea tarda G281E mutation in the uroporphyrinogen decarboxylase gene
Title: Hepatoerythropoietic porphyria and familial porphyria cutanea tarda in Spanish patients: G281E mutation in the uroporphyrinogen decarboxylase gene.
function of Arg37 in uroporphyrinogen III decarboxylase
Title: A tale of two acids: when arginine is a more appropriate acid than H3O+.
description of 3 siblings with hepatoerythropoietic porphyria; sequencing of the UROD gene revealed compound heterozygosity for a novel missense mutation, V166A, and a complex deletion/insertion, 645del1053ins10
Title: Hepatoerythropoietic porphyria misdiagnosed as child abuse: cutaneous, arthritic, and hematologic manifestations in siblings with a novel UROD mutation.

Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Familial porphyria cutanea tarda MedGen: C0268323 OMIM: 176100 GeneReviews: Familial Porphyria Cutanea Tarda, Hepatoerythropoietic Porphyria	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpu	vpu	HIV-1 Vpu-expressing U937 monocytes coculture with LX2 stellate cells to upregulate expression of profibrogenic markers COL-1, PCT, SMA-1, VEGF, and MMP2, which is inhibited by MIF treatment	PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

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Heme Biosynthesis, organism-specific biosystem (from WikiPathways)
Heme Biosynthesis, organism-specific biosystemThe enzymatic process that produces heme is properly called porphyrin synthesis, as all the intermediates are tetrapyrroles that are chemically classified are porphyrins. The process is highly conser...
Heme biosynthesis, organism-specific biosystem (from REACTOME)
Heme biosynthesis, organism-specific biosystemEight enzymes are involved in heme biosynthesis, four each in the mitochondria and the cytosol. The process starts in the mitochondria with the condensation of succinyl CoA (from the TCA cycle) and g...
Metabolic pathways, organism-specific biosystem (from KEGG)
Metabolic pathways, organism-specific biosystem
Metabolic pathways
Metabolism, organism-specific biosystem (from REACTOME)
Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
Metabolism of porphyrins, organism-specific biosystem (from REACTOME)
Metabolism of porphyrins, organism-specific biosystemPorphyrins are heterocyclic macrocycles, consisting of four pyrrole subunits (tetrapyrrole) linked by four methine (=CH-) bridges. The extensive conjugated porphyrin macrocycle is chromatic and the n...
Porphyrin and chlorophyll metabolism, organism-specific biosystem (from KEGG)
Porphyrin and chlorophyll metabolism, organism-specific biosystem
Porphyrin and chlorophyll metabolism
Porphyrin and chlorophyll metabolism, conserved biosystem (from KEGG)
Porphyrin and chlorophyll metabolism, conserved biosystem
Porphyrin and chlorophyll metabolism

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-74688 (e-PCR)
- UniSTS:43283

RH78894 (e-PCR)
- UniSTS:47380

WI-18590 (e-PCR)
- UniSTS:22821

MARC_6909-6910:992007560:1 (e-PCR)
- UniSTS:231286

MARC_6909-6910:996689833:1 (e-PCR)
- UniSTS:231286

MARC_14579-14580:1009487818:7 (e-PCR)
- UniSTS:267710

Homology

Homologs of the UROD gene: The UROD gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, N.crassa, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 255 organisms have orthologs with human gene UROD
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
protein binding	IPI Inferred from Physical Interaction more info	PubMed
uroporphyrinogen decarboxylase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
uroporphyrinogen decarboxylase activity	IDA Inferred from Direct Assay more info	PubMed
uroporphyrinogen decarboxylase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
heme biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
heme biosynthetic process	IC Inferred by Curator more info	PubMed
heme biosynthetic process	TAS Traceable Author Statement more info
protoporphyrinogen IX biosynthetic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
cytosol	IBA Inferred from Biological aspect of Ancestor more info	PubMed
cytosol	IDA Inferred from Direct Assay more info
cytosol	TAS Traceable Author Statement more info
nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: uroporphyrinogen decarboxylase

Names: uroporphyrinogen III decarboxylase

NP_000365.3

EC 4.1.1.37

XP_005271226.1

EC 4.1.1.37

XP_005271227.1

EC 4.1.1.37

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_007122.2 RefSeqGene

Range

5097..8418

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1079

mRNA and Protein(s)

NM_000374.5 → NP_000365.3 uroporphyrinogen decarboxylase

See identical proteins and their annotated locations for NP_000365.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shortest transcript and encodes the functional protein.

Source sequence(s)

AK291877, AL359473

Consensus CDS

CCDS518.1

UniProtKB/Swiss-Prot

P06132

Related

ENSP00000246337.4, ENST00000246337.8

Conserved Domains (1) summary

cd00717
Location:20 → 359

URO-D; Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction ...

RNA

NR_036510.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF104423, AK225053, AK291877, AL359473, DB462002
NR_158184.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL359473
NR_158185.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL359473

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p12 Primary Assembly

Range

45012133..45015669

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005271169.1 → XP_005271226.1 uroporphyrinogen decarboxylase isoform X1

Conserved Domains (1) summary

cd00717
Location:17 → 287

URO-D; Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction ...
XM_005271170.1 → XP_005271227.1 uroporphyrinogen decarboxylase isoform X1

Conserved Domains (1) summary

cd00717
Location:17 → 287

URO-D; Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction ...