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Protein

GDP-mannose mannosyl hydrolase

Gene

gmm

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Hydrolyzes both GDP-mannose and GDP-glucose. Could participate in the regulation of cell wall biosynthesis by influencing the concentration of GDP-mannose or GDP-glucose in the cell. Might also be involved in the biosynthesis of the slime polysaccharide colanic acid.2 Publications

Catalytic activityi

GDP-D-mannose + H2O = GDP + D-mannose.UniRule annotation2 Publications

Cofactori

Mg2+UniRule annotation3 PublicationsNote: Binds 1 Mg2+ ion per subunit.UniRule annotation3 Publications

Kineticsi

GDP-alpha-D-mannose is likely to be the biological substrate, but the Kcat/KM obtained with GDP-alpha-D-glucose is very similar to that with GDP-alpha-D-mannose.

  1. KM=0.3 mM for GDP-mannose1 Publication
  2. KM=1.9 mM for GDP-glucose1 Publication
  1. Vmax=1.6 µmol/min/mg enzyme with GDP-mannose as substrate1 Publication
  2. Vmax=7.5 µmol/min/mg enzyme with GDP-glucose as substrate1 Publication

pH dependencei

Optimum pH is 9.3.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei8SubstrateUniRule annotation2 Publications1
Binding sitei36SubstrateUniRule annotation2 Publications1
Metal bindingi49Magnesium; via carbonyl oxygenUniRule annotation2 Publications1
Metal bindingi69MagnesiumUniRule annotation2 Publications1
Metal bindingi122MagnesiumUniRule annotation2 Publications1
Sitei123Critical for catalysis1

GO - Molecular functioni

  • GDP-glucosidase activity Source: EcoCyc
  • GDP-mannose mannosyl hydrolase activity Source: UniProtKB-HAMAP
  • magnesium ion binding Source: EcoCyc
  • manganese ion binding Source: EcoCyc

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Lipopolysaccharide biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:GDPMANMANHYDRO-MONOMER.
ECOL316407:JW5335-MONOMER.
MetaCyc:GDPMANMANHYDRO-MONOMER.
SABIO-RKP32056.

Names & Taxonomyi

Protein namesi
Recommended name:
GDP-mannose mannosyl hydrolaseUniRule annotation (EC:3.6.1.-UniRule annotation)
Short name:
GDPMHUniRule annotation
Alternative name(s):
Colanic acid biosynthesis protein WcaH
Gene namesi
Name:gmmUniRule annotation
Synonyms:nudD, wcaH, yefC
Ordered Locus Names:b2051, JW5335
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11789. gmm.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi21D → A: Increases Km for GDP-mannose 5-fold. Reduces activity 120-fold. 1 Publication1
Mutagenesisi21D → N: Increases Km for GDP-mannose 9-fold. Reduces activity 400-fold. 1 Publication1
Mutagenesisi36R → Q: Increases Km for GDP-mannose 9-fold. Reduces activity 24-fold. 1 Publication1
Mutagenesisi51R → K: Increases Km for GDP-mannose 40-fold. Reduces activity 10-fold. 1 Publication1
Mutagenesisi51R → Q: Increases Km for GDP-mannose 40-fold. Reduces activity 300-fold. 1 Publication1
Mutagenesisi64R → Q: Increases Km for GDP-mannose 80-fold. Reduces activity 24-fold. 1 Publication1
Mutagenesisi69E → Q: Increases Km for GDP-mannose 10-fold. Increases Km for magnesium 40-fold. Reduces activity 150-fold. 1
Mutagenesisi87H → Q: Increases Km for GDP-mannose 4-fold. Reduces activity 200-fold. 1 Publication1
Mutagenesisi101H → Q: Increases Km for GDP-mannose 14-fold. Reduces activity 7-fold. 1 Publication1
Mutagenesisi102Y → F: Increases Km for GDP-mannose 7-fold. Reduces activity 100-fold. 1 Publication1
Mutagenesisi123H → Q: Increases Km for GDP-mannose 5-fold. Reduces activity 2000-fold. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000569831 – 159GDP-mannose mannosyl hydrolaseAdd BLAST159

Proteomic databases

PaxDbiP32056.
PRIDEiP32056.

Interactioni

Subunit structurei

Homodimer.UniRule annotation3 Publications

Protein-protein interaction databases

BioGridi4261145. 369 interactors.
STRINGi511145.b2051.

Structurei

Secondary structure

1159
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 14Combined sources10
Beta strandi17 – 25Combined sources9
Beta strandi31 – 36Combined sources6
Beta strandi38 – 41Combined sources4
Beta strandi44 – 46Combined sources3
Beta strandi49 – 51Combined sources3
Helixi58 – 70Combined sources13
Helixi76 – 78Combined sources3
Beta strandi79 – 92Combined sources14
Beta strandi95 – 98Combined sources4
Beta strandi100 – 110Combined sources11
Helixi113 – 115Combined sources3
Beta strandi120 – 129Combined sources10
Helixi131 – 136Combined sources6
Beta strandi138 – 140Combined sources3
Helixi142 – 145Combined sources4
Helixi146 – 148Combined sources3
Helixi150 – 153Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1RYAX-ray1.30A/B1-159[»]
2GT2X-ray2.00A/B/C/D1-159[»]
2GT4X-ray2.30A/B/C1-159[»]
ProteinModelPortaliP32056.
SMRiP32056.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP32056.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini13 – 153Nudix hydrolaseUniRule annotationAdd BLAST141

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 3Substrate binding2

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi50 – 71Nudix boxAdd BLAST22

Sequence similaritiesi

Belongs to the Nudix hydrolase family.UniRule annotation
Contains 1 nudix hydrolase domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105FGF. Bacteria.
COG0494. LUCA.
HOGENOMiHOG000280400.
InParanoidiP32056.
KOiK03207.
OMAiHDNSRAY.
PhylomeDBiP32056.

Family and domain databases

CDDicd03430. GDPMH. 1 hit.
Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00941. GDPMH_gmm. 1 hit.
InterProiIPR033715. GDPMH.
IPR028613. GDPMH_Gmm.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PIRSFiPIRSF037599. GDPMH. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P32056-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFLRQEDFAT VVRSTPLVSL DFIVENSRGE FLLGKRTNRP AQGYWFVPGG
60 70 80 90 100
RVQKDETLEA AFERLTMAEL GLRLPITAGQ FYGVWQHFYD DNFSGTDFTT
110 120 130 140 150
HYVVLGFRFR VSEEELLLPD EQHDDYRWLT SDALLASDNV HANSRAYFLA

EKRTGVPGL
Length:159
Mass (Da):18,273
Last modified:March 27, 2002 - v2
Checksum:iC7ADFFC56AD6B32A
GO

Sequence cautioni

The sequence AAC77844 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Mass spectrometryi

Molecular mass is 18472±67 Da from positions 1 - 159. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38473 Genomic DNA. Translation: AAC77844.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75112.2.
AP009048 Genomic DNA. Translation: BAA15907.2.
PIRiE55239.
RefSeqiNP_416555.2. NC_000913.3.
WP_001393539.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75112; AAC75112; b2051.
BAA15907; BAA15907; BAA15907.
GeneIDi946559.
KEGGiecj:JW5335.
eco:b2051.
PATRICi32119435. VBIEscCol129921_2128.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38473 Genomic DNA. Translation: AAC77844.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75112.2.
AP009048 Genomic DNA. Translation: BAA15907.2.
PIRiE55239.
RefSeqiNP_416555.2. NC_000913.3.
WP_001393539.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1RYAX-ray1.30A/B1-159[»]
2GT2X-ray2.00A/B/C/D1-159[»]
2GT4X-ray2.30A/B/C1-159[»]
ProteinModelPortaliP32056.
SMRiP32056.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261145. 369 interactors.
STRINGi511145.b2051.

Proteomic databases

PaxDbiP32056.
PRIDEiP32056.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75112; AAC75112; b2051.
BAA15907; BAA15907; BAA15907.
GeneIDi946559.
KEGGiecj:JW5335.
eco:b2051.
PATRICi32119435. VBIEscCol129921_2128.

Organism-specific databases

EchoBASEiEB1737.
EcoGeneiEG11789. gmm.

Phylogenomic databases

eggNOGiENOG4105FGF. Bacteria.
COG0494. LUCA.
HOGENOMiHOG000280400.
InParanoidiP32056.
KOiK03207.
OMAiHDNSRAY.
PhylomeDBiP32056.

Enzyme and pathway databases

BioCyciEcoCyc:GDPMANMANHYDRO-MONOMER.
ECOL316407:JW5335-MONOMER.
MetaCyc:GDPMANMANHYDRO-MONOMER.
SABIO-RKP32056.

Miscellaneous databases

EvolutionaryTraceiP32056.
PROiP32056.

Family and domain databases

CDDicd03430. GDPMH. 1 hit.
Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00941. GDPMH_gmm. 1 hit.
InterProiIPR033715. GDPMH.
IPR028613. GDPMH_Gmm.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PIRSFiPIRSF037599. GDPMH. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGMM_ECOLI
AccessioniPrimary (citable) accession number: P32056
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: March 27, 2002
Last modified: November 2, 2016
This is version 129 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.