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Entry version 121 (07 Oct 2020)
Sequence version 1 (08 Nov 2005)
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Protein

GDP-mannose 4,6-dehydratase

Gene

gmd

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.UniRule annotation1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

NADP+UniRule annotation2 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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.1 Publication
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. GDP-mannose 4,6-dehydratase (gmd)
  2. GDP-L-fucose synthase (fcl), GDP-L-fucose synthase (fcl)
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.

Pathwayi: colanic acid biosynthesis

This protein is involved in the pathway colanic acid biosynthesis, which is part of Exopolysaccharide biosynthesis.1 Publication
View all proteins of this organism that are known to be involved in the pathway colanic acid biosynthesis and in Exopolysaccharide biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei101NADPUniRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei1331 Publication1
Active sitei135Nucleophile1 Publication1
Active sitei157Nucleophile1 Publication1
Binding sitei161NADPCurated1
Binding sitei187NADPUniRule annotation1
Binding sitei192NADPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi9 – 14NADPUniRule annotation6
Nucleotide bindingi64 – 65NADPUniRule annotation2
Nucleotide bindingi86 – 90NADPUniRule annotation5

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionLyase
LigandNADP

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:GDPMANDEHYDRA-MONOMER
MetaCyc:GDPMANDEHYDRA-MONOMER

SABIO-RK: Biochemical Reaction Kinetics Database

More...
SABIO-RKi
P0AC88

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00128;UER00190
UPA00980

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
GDP-mannose 4,6-dehydrataseUniRule annotation (EC:4.2.1.47UniRule annotation)
Alternative name(s):
GDP-D-mannose dehydrataseUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:gmdUniRule annotation
Synonyms:yefA, yefN
Ordered Locus Names:b2053, JW2038
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi133T → V: Strongly reduces activity. 1 Publication1
Mutagenesisi135E → Q: Strongly reduces activity. 1 Publication1
Mutagenesisi157Y → F: Strongly reduces activity. 1 Publication1
Mutagenesisi161K → A: Strongly reduces activity. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002017121 – 373GDP-mannose 4,6-dehydrataseAdd BLAST373

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P0AC88

PRoteomics IDEntifications database

More...
PRIDEi
P0AC88

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4259690, 193 interactors

Database of interacting proteins

More...
DIPi
DIP-48216N

Protein interaction database and analysis system

More...
IntActi
P0AC88, 2 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b2053

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1373
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P0AC88

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P0AC88

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG1089, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_007383_14_0_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P0AC88

KEGG Orthology (KO)

More...
KOi
K01711

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P0AC88

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_00955, GDP_Man_dehydratase, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR006368, GDP_Man_deHydtase
IPR016040, NAD(P)-bd_dom
IPR036291, NAD(P)-bd_dom_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF16363, GDP_Man_Dehyd, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF51735, SSF51735, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR01472, gmd, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P0AC88-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSKVALITGV TGQDGSYLAE FLLEKGYEVH GIKRRASSFN TERVDHIYQD
60 70 80 90 100
PHTCNPKFHL HYGDLSDTSN LTRILREVQP DEVYNLGAMS HVAVSFESPE
110 120 130 140 150
YTADVDAMGT LRLLEAIRFL GLEKKTRFYQ ASTSELYGLV QEIPQKETTP
160 170 180 190 200
FYPRSPYAVA KLYAYWITVN YRESYGMYAC NGILFNHESP RRGETFVTRK
210 220 230 240 250
ITRAIANIAQ GLESCLYLGN MDSLRDWGHA KDYVKMQWMM LQQEQPEDFV
260 270 280 290 300
IATGVQYSVR QFVEMAAAQL GIKLRFEGTG VEEKGIVVSV TGHDAPGVKP
310 320 330 340 350
GDVIIAVDPR YFRPAEVETL LGDPTKAHEK LGWKPEITLR EMVSEMVAND
360 370
LEAAKKHSLL KSHGYDVAIA LES
Length:373
Mass (Da):42,047
Last modified:November 8, 2005 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i1A9BA2A7C566DE11
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U38473 Genomic DNA Translation: AAC77842.1
U00096 Genomic DNA Translation: AAC75114.1
AP009048 Genomic DNA Translation: BAA15909.1

Protein sequence database of the Protein Information Resource

More...
PIRi
D64971

NCBI Reference Sequences

More...
RefSeqi
NP_416557.1, NC_000913.3
WP_000048190.1, NZ_STEB01000002.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC75114; AAC75114; b2053
BAA15909; BAA15909; BAA15909

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
52077339
946562

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW2038
eco:b2053

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.198

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38473 Genomic DNA Translation: AAC77842.1
U00096 Genomic DNA Translation: AAC75114.1
AP009048 Genomic DNA Translation: BAA15909.1
PIRiD64971
RefSeqiNP_416557.1, NC_000913.3
WP_000048190.1, NZ_STEB01000002.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DB3X-ray2.30A2-373[»]
SMRiP0AC88
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4259690, 193 interactors
DIPiDIP-48216N
IntActiP0AC88, 2 interactors
STRINGi511145.b2053

Proteomic databases

PaxDbiP0AC88
PRIDEiP0AC88

Genome annotation databases

EnsemblBacteriaiAAC75114; AAC75114; b2053
BAA15909; BAA15909; BAA15909
GeneIDi52077339
946562
KEGGiecj:JW2038
eco:b2053
PATRICifig|1411691.4.peg.198

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB1735

Phylogenomic databases

eggNOGiCOG1089, Bacteria
HOGENOMiCLU_007383_14_0_6
InParanoidiP0AC88
KOiK01711
PhylomeDBiP0AC88

Enzyme and pathway databases

UniPathwayiUPA00128;UER00190
UPA00980
BioCyciEcoCyc:GDPMANDEHYDRA-MONOMER
MetaCyc:GDPMANDEHYDRA-MONOMER
SABIO-RKiP0AC88

Miscellaneous databases

EvolutionaryTraceiP0AC88

Protein Ontology

More...
PROi
PR:P0AC88

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
PfamiView protein in Pfam
PF16363, GDP_Man_Dehyd, 1 hit
SUPFAMiSSF51735, SSF51735, 1 hit
TIGRFAMsiTIGR01472, gmd, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiGM4D_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P0AC88
Secondary accession number(s): P32054, P77687
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: November 8, 2005
Last modified: October 7, 2020
This is version 121 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families
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