P32056 (GMM_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
GDP-mannose mannosyl hydrolase
Short name=GDPMH
EC=3.6.1.-

Alternative name(s):
Colanic acid biosynthesis protein WcaH

Gene names

Name:	gmm
Synonyms:	nudD, wcaH, yefC
Ordered Locus Names:	b2051, JW5335

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	159 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.6 Ref.7
Catalytic activity	GDP-D-mannose + H2O = GDP + D-mannose. Ref.6 Ref.7
Cofactor	Binds 1 magnesium ion per subunit. Ref.7 Ref.8 Ref.10
Subunit structure	Homodimer. Ref.7 Ref.10
Sequence similarities	Belongs to the Nudix hydrolase family. Contains 1 nudix hydrolase domain.
Biophysicochemical properties	Kinetic parameters: 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. KM=0.3 mM for GDP-mannose Ref.6 KM=1.9 mM for GDP-glucose Vmax=1.6 µmol/min/mg enzyme with GDP-mannose as substrate Vmax=7.5 µmol/min/mg enzyme with GDP-glucose as substrate pH dependence: Optimum pH is 9.3.
Mass spectrometry	Molecular mass is 18472±67 Da from positions 1 - 159. Determined by MALDI. Ref.7
Sequence caution	The sequence AAC77844.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Lipopolysaccharide biosynthesis
Ligand	Magnesium Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	lipopolysaccharide biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	GDP-glucosidase activity Inferred from direct assay Ref.6. Source: EcoCyc GDP-mannose mannosyl hydrolase activity Inferred from electronic annotation. Source: InterPro magnesium ion binding Inferred from mutant phenotype Ref.8. Source: EcoCyc manganese ion binding Inferred from mutant phenotype Ref.8. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 159

159

GDP-mannose mannosyl hydrolase HAMAP-Rule MF_00941

PRO_0000056983

Regions

Domain

13 – 153

141

Nudix hydrolase

Region

2 – 3

2

Substrate binding HAMAP-Rule MF_00941

Motif

50 – 71

22

Nudix box HAMAP-Rule MF_00941

Sites

Metal binding

49

1

Magnesium; via carbonyl oxygen

Metal binding

69

1

Magnesium

Metal binding

122

1

Magnesium

Binding site

8

1

Substrate

Binding site

36

1

Substrate

Site

123

1

Critical for catalysis

Experimental info

Mutagenesis

21

1

D → A: Increases Km for GDP-mannose 5-fold. Reduces activity 120-fold. Ref.9

Mutagenesis

21

1

D → N: Increases Km for GDP-mannose 9-fold. Reduces activity 400-fold. Ref.9

Mutagenesis

36

1

R → Q: Increases Km for GDP-mannose 9-fold. Reduces activity 24-fold. Ref.9

Mutagenesis

51

1

R → K: Increases Km for GDP-mannose 40-fold. Reduces activity 10-fold. Ref.8

Mutagenesis

51

1

R → Q: Increases Km for GDP-mannose 40-fold. Reduces activity 300-fold. Ref.8

Mutagenesis

64

1

R → Q: Increases Km for GDP-mannose 80-fold. Reduces activity 24-fold. Ref.8

Mutagenesis

69

1

E → Q: Increases Km for GDP-mannose 10-fold. Increases Km for magnesium 40-fold. Reduces activity 150-fold.

Mutagenesis

87

1

H → Q: Increases Km for GDP-mannose 4-fold. Reduces activity 200-fold. Ref.8

Mutagenesis

101

1

H → Q: Increases Km for GDP-mannose 14-fold. Reduces activity 7-fold. Ref.8

Mutagenesis

102

1

Y → F: Increases Km for GDP-mannose 7-fold. Reduces activity 100-fold. Ref.9

Mutagenesis

123

1

H → Q: Increases Km for GDP-mannose 5-fold. Reduces activity 2000-fold. Ref.8

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

159

Helix Strand Turn

Details...

Helix

5 – 14

10

Beta strand

17 – 25

9

Beta strand

31 – 36

6

Beta strand

38 – 41

4

Beta strand

44 – 46

3

Beta strand

49 – 51

3

Helix

58 – 70

13

Helix

76 – 78

3

Beta strand

79 – 92

14

Beta strand

95 – 98

4

Beta strand

100 – 110

11

Helix

113 – 115

3

Beta strand

120 – 129

10

Helix

131 – 136

6

Beta strand

138 – 140

3

Helix

142 – 145

4

Helix

146 – 148

3

Helix

150 – 153

4

Sequences

	Sequence		Length	Mass (Da)
	P32056 [UniParc]. Last modified March 27, 2002. Version 2. Checksum: C7ADFFC56AD6B32A	FASTA	159	18,273
	10 20 30 40 50 60 MFLRQEDFAT VVRSTPLVSL DFIVENSRGE FLLGKRTNRP AQGYWFVPGG RVQKDETLEA 70 80 90 100 110 120 AFERLTMAEL GLRLPITAGQ FYGVWQHFYD DNFSGTDFTT HYVVLGFRFR VSEEELLLPD 130 140 150 EQHDDYRWLT SDALLASDNV HANSRAYFLA EKRTGVPGL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map." Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S. , Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:379-392(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U38473 Genomic DNA. Translation: AAC77844.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75112.2.
AP009048 Genomic DNA. Translation: BAA15907.2.

PIR

E55239.

RefSeq

NP_416555.2. NC_000913.2.
YP_490293.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1RYA	X-ray	1.30	A/B	1-159	[»]
2GT2	X-ray	2.00	A/B/C/D	1-159	[»]
2GT4	X-ray	2.30	A/B/C	1-159	[»]

ProteinModelPortal

P32056.

SMR

P32056. Positions 1-159.

ModBase

Search...

Protein-protein interaction databases

STRING

511145.b2051.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75112; AAC75112; b2051.
BAA15907; BAA15907; BAA15907.

GeneID

12932151.
946559.

KEGG

ecj:Y75_p2014.
eco:b2051.

PATRIC

32119435. VBIEscCol129921_2128.

Organism-specific databases

EchoBASE

EB1737.

EcoGene

EG11789. gmm.

Phylogenomic databases

eggNOG

COG0494.

HOGENOM

HOG000280400.

KO

K03207.

OMA

MMFLRQE.

ProtClustDB

PRK15434.

Enzyme and pathway databases

BioCyc

EcoCyc:GDPMANMANHYDRO-MONOMER.
ECOL316407:JW5335-MONOMER.
MetaCyc:GDPMANMANHYDRO-MONOMER.

Gene expression databases

Genevestigator

P32056.

Family and domain databases

Gene3D

3.90.79.10. 1 hit.

HAMAP

MF_00941. GDPMH_gmm.

InterPro

IPR021161. Colanic_acid_synth_WcaH.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]

Pfam

PF00293. NUDIX. 1 hit.
[Graphical view]

PIRSF

PIRSF037599. GDPMH. 1 hit.

SUPFAM

SSF55811. NUDIX_hydrolase. 1 hit.

PROSITE

PS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P32056.

Entry information

Entry name

GMM_ECOLI

Accession

Primary (citable) accession number: P32056

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	March 27, 2002
Last modified:	May 1, 2013
This is version 108 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program