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Protein

GDP-mannose 4,6 dehydratase

Gene

GMDS

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

Functioni

Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.

Catalytic activityi

GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O.

Cofactori

NADP+1 Publication

Pathwayi: GDP-L-fucose biosynthesis via de novo pathway

This protein is involved in step 1 of the subpathway that synthesizes GDP-L-fucose from GDP-alpha-D-mannose.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. GDP-mannose 4,6 dehydratase (GMDS)
  2. GDP-L-fucose synthase (TSTA3)
This subpathway is part of the pathway GDP-L-fucose biosynthesis via de novo pathway, which is itself part of Nucleotide-sugar biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes GDP-L-fucose from GDP-alpha-D-mannose, the pathway GDP-L-fucose biosynthesis via de novo pathway and in Nucleotide-sugar biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei123NADP1 Publication1
Active sitei155By similarity1
Active sitei157NucleophileBy similarity1
Active sitei179NucleophileBy similarity1
Binding sitei183NADP1 Publication1
Binding sitei209NADP1 Publication1
Binding sitei214NADP1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi30 – 35NADP1 Publication6
Nucleotide bindingi55 – 58NADP1 Publication4
Nucleotide bindingi86 – 87NADP1 Publication2
Nucleotide bindingi108 – 112NADP1 Publication5

GO - Molecular functioni

  • GDP-mannose 4,6-dehydratase activity Source: UniProtKB
  • identical protein binding Source: IntAct
  • NADP+ binding Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionLyase
LigandNADP

Enzyme and pathway databases

BRENDAi4.2.1.47 2681
ReactomeiR-HSA-6787639 GDP-fucose biosynthesis
UniPathwayi
UPA00128;UER00190

Names & Taxonomyi

Protein namesi
Recommended name:
GDP-mannose 4,6 dehydratase (EC:4.2.1.47)
Alternative name(s):
GDP-D-mannose dehydratase
Short name:
GMD
Gene namesi
Name:GMDS
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000112699.10
HGNCiHGNC:4369 GMDS
MIMi602884 gene
neXtProtiNX_O60547

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

Pathology & Biotechi

Organism-specific databases

DisGeNETi2762
OpenTargetsiENSG00000112699
PharmGKBiPA28754

Chemistry databases

DrugBankiDB04315 Guanosine-5'-Diphosphate
DB02547 Guanosine-5'-Diphosphate-Rhamnose

Polymorphism and mutation databases

BioMutaiGMDS

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00002017052 – 372GDP-mannose 4,6 dehydrataseAdd BLAST371

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei323PhosphotyrosineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiO60547
MaxQBiO60547
PaxDbiO60547
PeptideAtlasiO60547
PRIDEiO60547
ProteomicsDBi49465

PTM databases

iPTMnetiO60547
PhosphoSitePlusiO60547

Expressioni

Gene expression databases

BgeeiENSG00000112699 Expressed in 207 organ(s), highest expression level in parotid gland
CleanExiHS_GMDS
GenevisibleiO60547 HS

Organism-specific databases

HPAiHPA031528

Interactioni

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi109024, 35 interactors
IntActiO60547, 15 interactors
STRINGi9606.ENSP00000370194

Structurei

Secondary structure

1372
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO60547
SMRiO60547
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO60547

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1372 Eukaryota
COG1089 LUCA
GeneTreeiENSGT00440000033640
HOGENOMiHOG000168003
HOVERGENiHBG000727
InParanoidiO60547
KOiK01711
OMAiTDCLYLG
OrthoDBiEOG091G093Z
PhylomeDBiO60547
TreeFamiTF300682

Family and domain databases

HAMAPiMF_00955 GDP_Man_dehydratase, 1 hit
InterProiView protein in InterPro
IPR006368 GDP_Man_deHydtase
IPR016040 NAD(P)-bd_dom
IPR036291 NAD(P)-bd_dom_sf
PANTHERiPTHR43715 PTHR43715, 1 hit
PfamiView protein in Pfam
PF16363 GDP_Man_Dehyd, 1 hit
SUPFAMiSSF51735 SSF51735, 1 hit
TIGRFAMsiTIGR01472 gmd, 1 hit

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: O60547-1) [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
MAHAPARCPS ARGSGDGEMG KPRNVALITG ITGQDGSYLA EFLLEKGYEV
60 70 80 90 100
HGIVRRSSSF NTGRIEHLYK NPQAHIEGNM KLHYGDLTDS TCLVKIINEV
110 120 130 140 150
KPTEIYNLGA QSHVKISFDL AEYTADVDGV GTLRLLDAVK TCGLINSVKF
160 170 180 190 200
YQASTSELYG KVQEIPQKET TPFYPRSPYG AAKLYAYWIV VNFREAYNLF
210 220 230 240 250
AVNGILFNHE SPRRGANFVT RKISRSVAKI YLGQLECFSL GNLDAKRDWG
260 270 280 290 300
HAKDYVEAMW LMLQNDEPED FVIATGEVHS VREFVEKSFL HIGKTIVWEG
310 320 330 340 350
KNENEVGRCK ETGKVHVTVD LKYYRPTEVD FLQGDCTKAK QKLNWKPRVA
360 370
FDELVREMVH ADVELMRTNP NA
Length:372
Mass (Da):41,950
Last modified:August 1, 1998 - v1
Checksum:iB1BAC441736D4C2B
GO
Isoform 2 (identifier: O60547-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-34: MAHAPARCPSARGSGDGEMGKPRNVALITGITGQ → MCKM

Note: No experimental confirmation available.
Show »
Length:342
Mass (Da):39,054
Checksum:iED43224234CC0A7B
GO

Sequence cautioni

The sequence AAC24501 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti156S → N in CAG46745 (Ref. 3) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0473241 – 34MAHAP…GITGQ → MCKM in isoform 2. 1 PublicationAdd BLAST34

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF042377 mRNA Translation: AAC13553.1
AF040260 mRNA Translation: AAC24501.1 Different initiation.
CR541929 mRNA Translation: CAG46727.1
CR541947 mRNA Translation: CAG46745.1
AL033517 Genomic DNA No translation available.
AL034344 Genomic DNA No translation available.
AL035693 Genomic DNA No translation available.
AL137179 Genomic DNA No translation available.
AL158139 Genomic DNA No translation available.
AL354670 Genomic DNA No translation available.
AL451141 Genomic DNA No translation available.
AL591048 Genomic DNA No translation available.
BC000117 mRNA Translation: AAH00117.1
CCDSiCCDS4474.1 [O60547-1]
CCDS58994.1 [O60547-2]
RefSeqiNP_001240775.1, NM_001253846.1 [O60547-2]
NP_001491.1, NM_001500.3 [O60547-1]
UniGeneiHs.144496
Hs.660919

Genome annotation databases

EnsembliENST00000380815; ENSP00000370194; ENSG00000112699 [O60547-1]
ENST00000530927; ENSP00000436726; ENSG00000112699 [O60547-2]
GeneIDi2762
KEGGihsa:2762
UCSCiuc003mtq.4 human [O60547-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF042377 mRNA Translation: AAC13553.1
AF040260 mRNA Translation: AAC24501.1 Different initiation.
CR541929 mRNA Translation: CAG46727.1
CR541947 mRNA Translation: CAG46745.1
AL033517 Genomic DNA No translation available.
AL034344 Genomic DNA No translation available.
AL035693 Genomic DNA No translation available.
AL137179 Genomic DNA No translation available.
AL158139 Genomic DNA No translation available.
AL354670 Genomic DNA No translation available.
AL451141 Genomic DNA No translation available.
AL591048 Genomic DNA No translation available.
BC000117 mRNA Translation: AAH00117.1
CCDSiCCDS4474.1 [O60547-1]
CCDS58994.1 [O60547-2]
RefSeqiNP_001240775.1, NM_001253846.1 [O60547-2]
NP_001491.1, NM_001500.3 [O60547-1]
UniGeneiHs.144496
Hs.660919

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1T2AX-ray1.84A/B/C/D23-372[»]
5IN4X-ray1.60A/B/C/D23-372[»]
5IN5X-ray1.90A/B/C/D23-372[»]
6GPJX-ray1.94A/B/C/D23-372[»]
6GPKX-ray1.47A/B/C/D23-372[»]
6GPLX-ray1.76B/C/D/E23-372[»]
ProteinModelPortaliO60547
SMRiO60547
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109024, 35 interactors
IntActiO60547, 15 interactors
STRINGi9606.ENSP00000370194

Chemistry databases

DrugBankiDB04315 Guanosine-5'-Diphosphate
DB02547 Guanosine-5'-Diphosphate-Rhamnose

PTM databases

iPTMnetiO60547
PhosphoSitePlusiO60547

Polymorphism and mutation databases

BioMutaiGMDS

Proteomic databases

EPDiO60547
MaxQBiO60547
PaxDbiO60547
PeptideAtlasiO60547
PRIDEiO60547
ProteomicsDBi49465

Protocols and materials databases

DNASUi2762
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000380815; ENSP00000370194; ENSG00000112699 [O60547-1]
ENST00000530927; ENSP00000436726; ENSG00000112699 [O60547-2]
GeneIDi2762
KEGGihsa:2762
UCSCiuc003mtq.4 human [O60547-1]

Organism-specific databases

CTDi2762
DisGeNETi2762
EuPathDBiHostDB:ENSG00000112699.10
GeneCardsiGMDS
HGNCiHGNC:4369 GMDS
HPAiHPA031528
MIMi602884 gene
neXtProtiNX_O60547
OpenTargetsiENSG00000112699
PharmGKBiPA28754
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1372 Eukaryota
COG1089 LUCA
GeneTreeiENSGT00440000033640
HOGENOMiHOG000168003
HOVERGENiHBG000727
InParanoidiO60547
KOiK01711
OMAiTDCLYLG
OrthoDBiEOG091G093Z
PhylomeDBiO60547
TreeFamiTF300682

Enzyme and pathway databases

UniPathwayi
UPA00128;UER00190

BRENDAi4.2.1.47 2681
ReactomeiR-HSA-6787639 GDP-fucose biosynthesis

Miscellaneous databases

ChiTaRSiGMDS human
EvolutionaryTraceiO60547
GeneWikiiGMDS_(gene)
GenomeRNAii2762
PROiPR:O60547
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000112699 Expressed in 207 organ(s), highest expression level in parotid gland
CleanExiHS_GMDS
GenevisibleiO60547 HS

Family and domain databases

HAMAPiMF_00955 GDP_Man_dehydratase, 1 hit
InterProiView protein in InterPro
IPR006368 GDP_Man_deHydtase
IPR016040 NAD(P)-bd_dom
IPR036291 NAD(P)-bd_dom_sf
PANTHERiPTHR43715 PTHR43715, 1 hit
PfamiView protein in Pfam
PF16363 GDP_Man_Dehyd, 1 hit
SUPFAMiSSF51735 SSF51735, 1 hit
TIGRFAMsiTIGR01472 gmd, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiGMDS_HUMAN
AccessioniPrimary (citable) accession number: O60547
Secondary accession number(s): E9PI88
, O75357, Q5T954, Q6FH09, Q9UGZ3, Q9UJK9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: August 1, 1998
Last modified: October 10, 2018
This is version 174 of the entry and version 1 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 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. SIMILARITY comments
    Index of protein domains and families
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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