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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei8 – 81SubstrateUniRule annotation2 Publications
Binding sitei36 – 361SubstrateUniRule annotation2 Publications
Metal bindingi49 – 491Magnesium; via carbonyl oxygenUniRule annotation2 Publications
Metal bindingi69 – 691MagnesiumUniRule annotation2 Publications
Metal bindingi122 – 1221MagnesiumUniRule annotation2 Publications
Sitei123 – 1231Critical for catalysis

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11789. gmm.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi21 – 211D → A: Increases Km for GDP-mannose 5-fold. Reduces activity 120-fold. 1 Publication
Mutagenesisi21 – 211D → N: Increases Km for GDP-mannose 9-fold. Reduces activity 400-fold. 1 Publication
Mutagenesisi36 – 361R → Q: Increases Km for GDP-mannose 9-fold. Reduces activity 24-fold. 1 Publication
Mutagenesisi51 – 511R → K: Increases Km for GDP-mannose 40-fold. Reduces activity 10-fold. 1 Publication
Mutagenesisi51 – 511R → Q: Increases Km for GDP-mannose 40-fold. Reduces activity 300-fold. 1 Publication
Mutagenesisi64 – 641R → Q: Increases Km for GDP-mannose 80-fold. Reduces activity 24-fold. 1 Publication
Mutagenesisi69 – 691E → Q: Increases Km for GDP-mannose 10-fold. Increases Km for magnesium 40-fold. Reduces activity 150-fold.
Mutagenesisi87 – 871H → Q: Increases Km for GDP-mannose 4-fold. Reduces activity 200-fold. 1 Publication
Mutagenesisi101 – 1011H → Q: Increases Km for GDP-mannose 14-fold. Reduces activity 7-fold. 1 Publication
Mutagenesisi102 – 1021Y → F: Increases Km for GDP-mannose 7-fold. Reduces activity 100-fold. 1 Publication
Mutagenesisi123 – 1231H → Q: Increases Km for GDP-mannose 5-fold. Reduces activity 2000-fold. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 159159GDP-mannose mannosyl hydrolasePRO_0000056983Add
BLAST

Proteomic databases

PaxDbiP32056.

Interactioni

Subunit structurei

Homodimer.UniRule annotation3 Publications

Protein-protein interaction databases

BioGridi4261145. 369 interactions.
STRINGi511145.b2051.

Structurei

Secondary structure

1
159
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 1410Combined sources
Beta strandi17 – 259Combined sources
Beta strandi31 – 366Combined sources
Beta strandi38 – 414Combined sources
Beta strandi44 – 463Combined sources
Beta strandi49 – 513Combined sources
Helixi58 – 7013Combined sources
Helixi76 – 783Combined sources
Beta strandi79 – 9214Combined sources
Beta strandi95 – 984Combined sources
Beta strandi100 – 11011Combined sources
Helixi113 – 1153Combined sources
Beta strandi120 – 12910Combined sources
Helixi131 – 1366Combined sources
Beta strandi138 – 1403Combined sources
Helixi142 – 1454Combined sources
Helixi146 – 1483Combined sources
Helixi150 – 1534Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP32056.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini13 – 153141Nudix hydrolaseUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni2 – 32Substrate binding

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi50 – 7122Nudix boxAdd
BLAST

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.
OrthoDBiEOG6038X1.
PhylomeDBiP32056.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00941. GDPMH_gmm.
InterProiIPR028613. 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 AAC77844.1 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
EntryMethodResolution (Å)ChainPositionsPDBsum
1RYAX-ray1.30A/B1-159[»]
2GT2X-ray2.00A/B/C/D1-159[»]
2GT4X-ray2.30A/B/C1-159[»]
ProteinModelPortaliP32056.
SMRiP32056. Positions 1-159.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261145. 369 interactions.
STRINGi511145.b2051.

Proteomic databases

PaxDbiP32056.

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.
OrthoDBiEOG6038X1.
PhylomeDBiP32056.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP32056.
PROiP32056.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00941. GDPMH_gmm.
InterProiIPR028613. 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...

Publicationsi

« Hide 'large scale' publications
  1. "Evidence for effect of random genetic drift on G+C content after lateral transfer of fucose pathway genes to Escherichia coli K-12."
    Aoyama K., Haase A.M., Reeves P.R.
    Mol. Biol. Evol. 11:829-838(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid."
    Stevenson G., Andrianopoulos K., Hobbs M., Reeves P.R.
    J. Bacteriol. 178:4885-4893(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "A novel GDP-mannose mannosyl hydrolase shares homology with the MutT family of enzymes."
    Frick D.N., Townsend B.D., Bessman M.J.
    J. Biol. Chem. 270:24086-24091(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: ATCC 33694 / HB101.
  7. "GDP-mannose mannosyl hydrolase catalyzes nucleophilic substitution at carbon, unlike all other Nudix hydrolases."
    Legler P.M., Massiah M.A., Bessman M.J., Mildvan A.S.
    Biochemistry 39:8603-8608(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, MASS SPECTROMETRY.
    Strain: ATCC 33694 / HB101.
  8. "Mutational, kinetic, and NMR studies of the mechanism of E. coli GDP-mannose mannosyl hydrolase, an unusual Nudix enzyme."
    Legler P.M., Massiah M.A., Mildvan A.S.
    Biochemistry 41:10834-10848(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ARG-51; ARG-64; HIS-87; HIS-101 AND HIS-123, COFACTOR.
  9. "Mutational, structural, and kinetic evidence for a dissociative mechanism in the GDP-mannose mannosyl hydrolase reaction."
    Xia Z., Azurmendi H.F., Lairson L.L., Withers S.G., Gabelli S.B., Bianchet M.A., Amzel L.M., Mildvan A.S.
    Biochemistry 44:8989-8997(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ASP-21; ARG-36 AND TYR-102.
  10. "Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus."
    Gabelli S.B., Bianchet M.A., Azurmendi H.F., Xia Z., Sarawat V., Mildvan A.S., Amzel L.M.
    Structure 12:927-935(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND MAGNESIUM, COFACTOR, SUBUNIT.
  11. "X-ray, NMR, and mutational studies of the catalytic cycle of the GDP-mannose mannosyl hydrolase reaction."
    Gabelli S.B., Azurmendi H.F., Bianchet M.A., Amzel L.M., Mildvan A.S.
    Biochemistry 45:11290-11303(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT PHE-102 IN COMPLEX WITH SUBSTRATE AND MAGNESIUM.

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: April 13, 2016
This is version 126 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.