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GMDS GDP-mannose 4,6-dehydratase [ Homo sapiens (human) ]

Gene ID: 2762, updated on 11-Sep-2019

Summary

Official Symbol
GMDSprovided by HGNC
Official Full Name
GDP-mannose 4,6-dehydrataseprovided by HGNC
Primary source
HGNC:HGNC:4369
See related
Ensembl:ENSG00000112699 MIM:602884
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GMD; SDR3E1
Summary
GDP-mannose 4,6-dehydratase (GMD; EC 4.2.1.47) catalyzes the conversion of GDP-mannose to GDP-4-keto-6-deoxymannose, the first step in the synthesis of GDP-fucose from GDP-mannose, using NADP+ as a cofactor. The second and third steps of the pathway are catalyzed by a single enzyme, GDP-keto-6-deoxymannose 3,5-epimerase, 4-reductase, designated FX in humans (MIM 137020).[supplied by OMIM, Aug 2009]
Expression
Broad expression in colon (RPKM 6.8), stomach (RPKM 6.6) and 23 other tissues See more
Orthologs

Genomic context

See GMDS in Genome Data Viewer
Location:
6p25.3
Exon count:
21
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (1623800..2245605, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (1624035..2245868, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986514 Neighboring gene FOXC1 upstream transcript Neighboring gene uncharacterized LOC107986513 Neighboring gene forkhead box C1 Neighboring gene uncharacterized LOC107986512 Neighboring gene GMDS divergent transcript Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 28 Neighboring gene long intergenic non-protein coding RNA 1600 Neighboring gene long intergenic non-protein coding RNA 2521

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma.
NHGRI GWA Catalog
Discovery and replication of dopamine-related gene effects on caudate volume in young and elderly populations (N=1198) using genome-wide search.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
Polymorphic markers associated with severe oxaliplatin-induced, chronic peripheral neuropathy in colon cancer patients.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of GDP-mannose 4,6-dehydratase (GMDS) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GDP-mannose 4,6-dehydratase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
GDP-mannose 4,6-dehydratase activity IDA
Inferred from Direct Assay
more info
PubMed 
GDP-mannose 4,6-dehydratase activity IGI
Inferred from Genetic Interaction
more info
PubMed 
GDP-mannose 4,6-dehydratase activity TAS
Traceable Author Statement
more info
 
NADP+ binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
'de novo' GDP-L-fucose biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
'de novo' GDP-L-fucose biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
'de novo' GDP-L-fucose biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
GDP-mannose metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
GDP-mannose metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
GDP-mannose metabolic process IGI
Inferred from Genetic Interaction
more info
PubMed 
Notch signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IC
Inferred by Curator
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 

General protein information

Preferred Names
GDP-mannose 4,6 dehydratase
Names
GDP-D-mannose dehydratase
short chain dehydrogenase/reductase family 3E, member 1
NP_001240775.1
NP_001491.1
XP_006715129.1
XP_011512802.1
XP_011512804.1
XP_011512805.1
XP_011512807.1
XP_011512808.1
XP_011512809.1
XP_016866241.1

NCBI Reference Sequences (RefSeq)

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.

mRNA and Protein(s)

  1. NM_001253846.1NP_001240775.1  GDP-mannose 4,6 dehydratase isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AF040260, AI761361
    Consensus CDS
    CCDS58994.1
    UniProtKB/Swiss-Prot
    O60547
    Related
    ENSP00000436726.1, ENST00000530927.5
    Conserved Domains (2) summary
    TIGR01472
    Location:5336
    gmd; GDP-mannose 4,6-dehydratase
    pfam16363
    Location:4328
    GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase
  2. NM_001500.4NP_001491.1  GDP-mannose 4,6 dehydratase isoform 1

    See identical proteins and their annotated locations for NP_001491.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AF042377, BM665440, BQ923510
    Consensus CDS
    CCDS4474.1
    UniProtKB/Swiss-Prot
    O60547
    Related
    ENSP00000370194.4, ENST00000380815.5
    Conserved Domains (1) summary
    TIGR01472
    Location:24366
    gmd; GDP-mannose 4,6-dehydratase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    1623800..2245605 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514500.1XP_011512802.1  GDP-mannose 4,6 dehydratase isoform X1

    Conserved Domains (2) summary
    TIGR01472
    Location:4336
    gmd; GDP-mannose 4,6-dehydratase
    pfam16363
    Location:5328
    GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase
  2. XM_017010752.1XP_016866241.1  GDP-mannose 4,6 dehydratase isoform X4

  3. XM_011514502.3XP_011512804.1  GDP-mannose 4,6 dehydratase isoform X2

    Conserved Domains (2) summary
    pfam16363
    Location:27329
    GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase
    cl21454
    Location:24329
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins
  4. XM_011514507.2XP_011512809.1  GDP-mannose 4,6 dehydratase isoform X8

    Conserved Domains (2) summary
    pfam16363
    Location:27216
    GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase
    cl21454
    Location:24215
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins
  5. XM_006715066.3XP_006715129.1  GDP-mannose 4,6 dehydratase isoform X3

    Conserved Domains (2) summary
    pfam01370
    Location:26257
    Epimerase; NAD dependent epimerase/dehydratase family
    cl21454
    Location:24257
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins
  6. XM_011514506.2XP_011512808.1  GDP-mannose 4,6 dehydratase isoform X7

    Conserved Domains (2) summary
    pfam16363
    Location:27217
    GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase
    cl21454
    Location:24214
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins
  7. XM_011514505.2XP_011512807.1  GDP-mannose 4,6 dehydratase isoform X6

    Conserved Domains (2) summary
    pfam16363
    Location:27217
    GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase
    cl21454
    Location:24214
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins
  8. XM_011514503.3XP_011512805.1  GDP-mannose 4,6 dehydratase isoform X5

    Conserved Domains (2) summary
    pfam16363
    Location:27217
    GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase
    cl21454
    Location:24214
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

RNA

  1. XR_001743349.2 RNA Sequence

  2. XR_001743350.2 RNA Sequence

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