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O60547 (GMDS_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
GDP-mannose 4,6 dehydratase

EC=4.2.1.47
Alternative name(s):
GDP-D-mannose dehydratase
Short name=GMD
Gene names
Name:GMDS
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length372 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose. HAMAP-Rule MF_00955

Catalytic activity

GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O. HAMAP-Rule MF_00955

Cofactor

NADP. Ref.8

Pathway

Nucleotide-sugar biosynthesis; GDP-L-fucose biosynthesis via de novo pathway; GDP-L-fucose from GDP-alpha-D-mannose: step 1/2. HAMAP-Rule MF_00955

Sequence similarities

Belongs to the NAD(P)-dependent epimerase/dehydratase family. GDP-mannose 4,6-dehydratase subfamily.

Sequence caution

The sequence AAC24501.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O60547-1)

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.
Isoform 2 (identifier: O60547-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-34: MAHAPARCPSARGSGDGEMGKPRNVALITGITGQ → MCKM
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.6
Chain2 – 372371GDP-mannose 4,6 dehydratase HAMAP-Rule MF_00955
PRO_0000201705

Regions

Nucleotide binding30 – 356NADP HAMAP-Rule MF_00955
Nucleotide binding55 – 584NADP HAMAP-Rule MF_00955
Nucleotide binding86 – 872NADP HAMAP-Rule MF_00955
Nucleotide binding108 – 1125NADP HAMAP-Rule MF_00955

Sites

Active site1551 By similarity
Active site1571Nucleophile By similarity
Active site1791Nucleophile By similarity
Binding site1231NADP
Binding site1831NADP
Binding site2091NADP
Binding site2141NADP

Amino acid modifications

Modified residue21N-acetylalanine Ref.6

Natural variations

Alternative sequence1 – 3434MAHAP…GITGQ → MCKM in isoform 2.
VSP_047324

Experimental info

Sequence conflict1561S → N in CAG46745. Ref.3

Secondary structure

............................................................ 372
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified August 1, 1998. Version 1.
Checksum: B1BAC441736D4C2B

FASTA37241,950
        10         20         30         40         50         60 
MAHAPARCPS ARGSGDGEMG KPRNVALITG ITGQDGSYLA EFLLEKGYEV HGIVRRSSSF 

        70         80         90        100        110        120 
NTGRIEHLYK NPQAHIEGNM KLHYGDLTDS TCLVKIINEV KPTEIYNLGA QSHVKISFDL 

       130        140        150        160        170        180 
AEYTADVDGV GTLRLLDAVK TCGLINSVKF YQASTSELYG KVQEIPQKET TPFYPRSPYG 

       190        200        210        220        230        240 
AAKLYAYWIV VNFREAYNLF AVNGILFNHE SPRRGANFVT RKISRSVAKI YLGQLECFSL 

       250        260        270        280        290        300 
GNLDAKRDWG HAKDYVEAMW LMLQNDEPED FVIATGEVHS VREFVEKSFL HIGKTIVWEG 

       310        320        330        340        350        360 
KNENEVGRCK ETGKVHVTVD LKYYRPTEVD FLQGDCTKAK QKLNWKPRVA FDELVREMVH 

       370 
ADVELMRTNP NA 

« Hide

Isoform 2 [UniParc].

Checksum: ED43224234CC0A7B
Show »

FASTA34239,054

References

« Hide 'large scale' references
[1]"Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro."
Sullivan F.X., Kumar R., Kriz R., Stahl M., Xu G.-Y., Rouse J., Chang X.J., Boodhoo A., Potvin B., Cumming D.A.
J. Biol. Chem. 273:8193-8202(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[2]"Molecular cloning and expression of GDP-D-mannose-4,6-dehydratase, a key enzyme for fucose metabolism defective in Lec13 cells."
Ohyama C., Smith P.L., Angata K., Fukuda M.N., Lowe J.B., Fukuda M.
J. Biol. Chem. 273:14582-14587(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
Tissue: Brain.
[3]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Halleck A., Ebert L., Mkoundinya M., Schick M., Eisenstein S., Neubert P., Kstrang K., Schatten R., Shen B., Henze S., Mar W., Korn B., Zuo D., Hu Y., LaBaer J.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[4]"The DNA sequence and analysis of human chromosome 6."
Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Eye.
[6]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
[7]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"Crystal structure and biophysical characterization of human GDP-D-mannose 4,6-dehydratase."
Vedadi M., Walker J.R., Sharma S., Houston S., Wasney G., Loppnau P., Oppermann U.
Submitted (APR-2004) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS) OF 23-372 IN COMPLEX WITH NADP, COFACTOR.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001240775.1. NM_001253846.1.
NP_001491.1. NM_001500.3.
UniGeneHs.144496.
Hs.660919.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1T2AX-ray1.84A/B/C/D23-372[»]
ProteinModelPortalO60547.
SMRO60547. Positions 23-369.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid109024. 12 interactions.
IntActO60547. 1 interaction.
STRING9606.ENSP00000370194.

PTM databases

PhosphoSiteO60547.

Proteomic databases

PaxDbO60547.
PeptideAtlasO60547.
PRIDEO60547.

Protocols and materials databases

DNASU2762.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000380815; ENSP00000370194; ENSG00000112699. [O60547-1]
ENST00000530927; ENSP00000436726; ENSG00000112699. [O60547-2]
GeneID2762.
KEGGhsa:2762.
UCSCuc003mtq.3. human. [O60547-1]

Organism-specific databases

CTD2762.
GeneCardsGC06M001624.
HGNCHGNC:4369. GMDS.
HPAHPA031528.
MIM602884. gene.
neXtProtNX_O60547.
PharmGKBPA28754.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1089.
HOGENOMHOG000168003.
HOVERGENHBG000727.
InParanoidO60547.
KOK01711.
OMATDCLYLG.
OrthoDBEOG7K6PV5.
PhylomeDBO60547.
TreeFamTF300682.

Enzyme and pathway databases

UniPathwayUPA00128; UER00190.

Gene expression databases

ArrayExpressO60547.
BgeeO60547.
CleanExHS_GMDS.
GenevestigatorO60547.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
HAMAPMF_00955. GDP_Man_dehydratase.
InterProIPR001509. Epimerase_deHydtase.
IPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamPF01370. Epimerase. 1 hit.
[Graphical view]
TIGRFAMsTIGR01472. gmd. 1 hit.
ProtoNetSearch...

Other

ChiTaRSGMDS. human.
EvolutionaryTraceO60547.
GeneWikiGMDS_(gene).
GenomeRNAi2762.
NextBio10866.
PROO60547.
SOURCESearch...

Entry information

Entry nameGMDS_HUMAN
AccessionPrimary (citable) accession number: O60547
Secondary accession number(s): E9PI88 expand/collapse secondary AC list , O75357, Q5T954, Q6FH09, Q9UGZ3, Q9UJK9
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: August 1, 1998
Last modified: March 19, 2014
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 6

Human chromosome 6: entries, gene names and cross-references to MIM