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O60547

- GMDS_HUMAN

UniProt

O60547 - GMDS_HUMAN

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Protein

GDP-mannose 4,6 dehydratase

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

Functioni

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

Catalytic activityi

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

Cofactori

NADP.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei123 – 1231NADP
Active sitei155 – 1551 By similarity
Active sitei157 – 1571Nucleophile By similarity
Active sitei179 – 1791Nucleophile By similarity
Binding sitei183 – 1831NADP
Binding sitei209 – 2091NADP
Binding sitei214 – 2141NADP

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi30 – 356NADPUniRule annotation
Nucleotide bindingi55 – 584NADPUniRule annotation
Nucleotide bindingi86 – 872NADPUniRule annotation
Nucleotide bindingi108 – 1125NADPUniRule annotation

GO - Molecular functioni

  1. GDP-mannose 4,6-dehydratase activity Source: UniProtKB
  2. NADP+ binding Source: UniProtKB

GO - Biological processi

  1. 'de novo' GDP-L-fucose biosynthetic process Source: UniProtKB
  2. GDP-mannose metabolic process Source: UniProtKB
  3. Notch signaling pathway Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

NADP

Enzyme and pathway databases

UniPathwayiUPA00128; 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
ProteomesiUP000005640: Chromosome 6

Organism-specific databases

HGNCiHGNC:4369. GMDS.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. extracellular vesicular exosome Source: UniProt
Complete GO annotation...

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA28754.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 372371GDP-mannose 4,6 dehydrataseUniRule annotationPRO_0000201705Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiO60547.
PaxDbiO60547.
PeptideAtlasiO60547.
PRIDEiO60547.

PTM databases

PhosphoSiteiO60547.

Expressioni

Gene expression databases

ArrayExpressiO60547.
BgeeiO60547.
CleanExiHS_GMDS.
GenevestigatoriO60547.

Organism-specific databases

HPAiHPA031528.

Interactioni

Protein-protein interaction databases

BioGridi109024. 12 interactions.
IntActiO60547. 1 interaction.
STRINGi9606.ENSP00000370194.

Structurei

Secondary structure

1
372
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi25 – 295
Turni30 – 323
Helixi34 – 4512
Beta strandi49 – 546
Turni63 – 653
Helixi66 – 683
Beta strandi80 – 845
Helixi90 – 10011
Beta strandi103 – 1075
Helixi114 – 1196
Helixi121 – 1288
Helixi130 – 14112
Turni145 – 1473
Beta strandi149 – 1557
Helixi156 – 1583
Beta strandi163 – 1675
Helixi178 – 19720
Beta strandi200 – 2067
Helixi219 – 23113
Beta strandi238 – 2414
Helixi252 – 26413
Beta strandi265 – 2673
Beta strandi271 – 2733
Helixi281 – 29111
Beta strandi296 – 3005
Helixi302 – 3043
Beta strandi306 – 3094
Turni310 – 3123
Beta strandi315 – 3195
Helixi321 – 3233
Helixi337 – 3437
Helixi351 – 36818

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1T2AX-ray1.84A/B/C/D23-372[»]
ProteinModelPortaliO60547.
SMRiO60547. Positions 23-369.

Miscellaneous databases

EvolutionaryTraceiO60547.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1089.
HOGENOMiHOG000168003.
HOVERGENiHBG000727.
InParanoidiO60547.
KOiK01711.
OMAiFMHIGKT.
OrthoDBiEOG7K6PV5.
PhylomeDBiO60547.
TreeFamiTF300682.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase.
InterProiIPR001509. Epimerase_deHydtase.
IPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF01370. Epimerase. 1 hit.
[Graphical view]
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. Align

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

MAHAPARCPS ARGSGDGEMG KPRNVALITG ITGQDGSYLA EFLLEKGYEV    50
HGIVRRSSSF NTGRIEHLYK NPQAHIEGNM KLHYGDLTDS TCLVKIINEV 100
KPTEIYNLGA QSHVKISFDL AEYTADVDGV GTLRLLDAVK TCGLINSVKF 150
YQASTSELYG KVQEIPQKET TPFYPRSPYG AAKLYAYWIV VNFREAYNLF 200
AVNGILFNHE SPRRGANFVT RKISRSVAKI YLGQLECFSL GNLDAKRDWG 250
HAKDYVEAMW LMLQNDEPED FVIATGEVHS VREFVEKSFL HIGKTIVWEG 300
KNENEVGRCK ETGKVHVTVD LKYYRPTEVD FLQGDCTKAK QKLNWKPRVA 350
FDELVREMVH ADVELMRTNP NA 372
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 AAC24501.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 3434MAHAP…GITGQ → MCKM in isoform 2. VSP_047324Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti156 – 1561S → N in CAG46745. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.3. human. [O60547-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS4474.1. [O60547-1 ]
CCDS58994.1. [O60547-2 ]
RefSeqi NP_001240775.1. NM_001253846.1. [O60547-2 ]
NP_001491.1. NM_001500.3. [O60547-1 ]
UniGenei Hs.144496.
Hs.660919.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1T2A X-ray 1.84 A/B/C/D 23-372 [» ]
ProteinModelPortali O60547.
SMRi O60547. Positions 23-369.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 109024. 12 interactions.
IntActi O60547. 1 interaction.
STRINGi 9606.ENSP00000370194.

PTM databases

PhosphoSitei O60547.

Proteomic databases

MaxQBi O60547.
PaxDbi O60547.
PeptideAtlasi O60547.
PRIDEi O60547.

Protocols and materials databases

DNASUi 2762.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000380815 ; ENSP00000370194 ; ENSG00000112699 . [O60547-1 ]
ENST00000530927 ; ENSP00000436726 ; ENSG00000112699 . [O60547-2 ]
GeneIDi 2762.
KEGGi hsa:2762.
UCSCi uc003mtq.3. human. [O60547-1 ]

Organism-specific databases

CTDi 2762.
GeneCardsi GC06M001624.
HGNCi HGNC:4369. GMDS.
HPAi HPA031528.
MIMi 602884. gene.
neXtProti NX_O60547.
PharmGKBi PA28754.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG1089.
HOGENOMi HOG000168003.
HOVERGENi HBG000727.
InParanoidi O60547.
KOi K01711.
OMAi FMHIGKT.
OrthoDBi EOG7K6PV5.
PhylomeDBi O60547.
TreeFami TF300682.

Enzyme and pathway databases

UniPathwayi UPA00128 ; UER00190 .

Miscellaneous databases

ChiTaRSi GMDS. human.
EvolutionaryTracei O60547.
GeneWikii GMDS_(gene).
GenomeRNAii 2762.
NextBioi 10866.
PROi O60547.
SOURCEi Search...

Gene expression databases

ArrayExpressi O60547.
Bgeei O60547.
CleanExi HS_GMDS.
Genevestigatori O60547.

Family and domain databases

Gene3Di 3.40.50.720. 1 hit.
HAMAPi MF_00955. GDP_Man_dehydratase.
InterProi IPR001509. Epimerase_deHydtase.
IPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
Pfami PF01370. Epimerase. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR01472. gmd. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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.

Entry informationi

Entry nameiGMDS_HUMAN
AccessioniPrimary (citable) accession number: O60547
Secondary accession number(s): E9PI88
, O75357, Q5T954, Q6FH09, Q9UGZ3, Q9UJK9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: August 1, 1998
Last modified: July 9, 2014
This is version 131 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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