P63224 (GMHA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Phosphoheptose isomerase
EC=5.3.1.28

Alternative name(s):
Sedoheptulose 7-phosphate isomerase

Gene names

Name:	gmhA
Synonyms:	lpcA, tfrA, yafI
Ordered Locus Names:	b0222, JW0212

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	192 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. Ref.7 Ref.10
Catalytic activity	D-sedoheptulose 7-phosphate = D-glycero-D-manno-heptose 7-phosphate. Ref.10
Cofactor	Binds 1 zinc ion per subunit By similarity.
Pathway	Carbohydrate biosynthesis; D-glycero-D-manno-heptose 7-phosphate biosynthesis; D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate from sedoheptulose 7-phosphate: step 1/1. Ref.7 Bacterial outer membrane biogenesis; LPS core biosynthesis. Ref.7
Subunit structure	Homotetramer. Ref.10
Subcellular location	Cytoplasm HAMAP-Rule MF_00067.
Miscellaneous	The reaction produces a racemic mixture of D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate. HAMAP-Rule MF_00067
Sequence similarities	Belongs to the SIS family. GmhA subfamily. Contains 1 SIS domain.
Sequence caution	The sequence AAB08644.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Carbohydrate metabolism Lipopolysaccharide biosynthesis
Cellular component	Cytoplasm
Ligand	Metal-binding Zinc
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	D-glycero-D-manno-heptose 7-phosphate biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway lipopolysaccharide core region biosynthetic process Inferred from mutant phenotype Ref.1. Source: EcoCyc
Cellular_component	cytoplasm Inferred from sequence or structural similarity Ref.1. Source: EcoCyc
Molecular_function	D-sedoheptulose 7-phosphate isomerase activity Inferred from direct assay Ref.10. Source: EcoCyc carbohydrate binding Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 192

192

Phosphoheptose isomerase HAMAP-Rule MF_00067

PRO_0000136526

Regions

Domain

37 – 192

156

SIS

Region

54 – 55

2

Substrate binding HAMAP-Rule MF_00067

Region

93 – 94

2

Substrate binding By similarity

Region

119 – 121

3

Substrate binding By similarity

Sites

Metal binding

61

1

Zinc By similarity

Metal binding

65

1

Zinc By similarity

Metal binding

172

1

Zinc By similarity

Metal binding

180

1

Zinc By similarity

Binding site

61

1

Substrate

Binding site

65

1

Substrate By similarity

Binding site

120

1

Substrate

Binding site

124

1

Substrate By similarity

Binding site

169

1

Substrate

Binding site

172

1

Substrate

Binding site

180

1

Substrate

Experimental info

Mutagenesis

61

1

H → Q: Almost no effect. Ref.10

Mutagenesis

65

1

E → N or Q: No activity. Ref.10

Mutagenesis

69

1

R → Q: Almost no effect. Ref.10

Mutagenesis

94

1

D → N: No activity. Ref.10

Mutagenesis

120

1

T → A: No activity. Ref.10

Mutagenesis

169

1

D → N: No activity. Ref.10

Mutagenesis

172

1

Q → E: No activity. Ref.10

Mutagenesis

180

1

H → Q: No activity. Ref.10

Secondary structure

1

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192

Helix Strand Turn

Details...

Helix

3 – 22

20

Helix

24 – 42

19

Beta strand

47 – 52

6

Helix

54 – 70

17

Beta strand

74 – 76

3

Beta strand

78 – 81

4

Helix

88 – 91

4

Helix

100 – 108

9

Beta strand

114 – 118

5

Beta strand

120 – 122

3

Helix

125 – 137

13

Beta strand

140 – 146

7

Helix

150 – 152

3

Beta strand

156 – 162

7

Helix

168 – 191

24

Sequences

	Sequence		Length	Mass (Da)
	P63224 [UniParc]. Last modified September 27, 2004. Version 1. Checksum: 7A2C05E1079108B4	FASTA	192	20,815
	10 20 30 40 50 60 MYQDLIRNEL NEAAETLANF LKDDANIHAI QRAAVLLADS FKAGGKVLSC GNGGSHCDAM 70 80 90 100 110 120 HFAEELTGRY RENRPGYPAI AISDVSHISC VGNDFGFNDI FSRYVEAVGR EGDVLLGIST 130 140 150 160 170 180 SGNSANVIKA IAAAREKGMK VITLTGKDGG KMAGTADIEI RVPHFGYADR IQEIHIKVIH 190 ILIQLIEKEM VK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Biosynthesis of inner core lipopolysaccharide in enteric bacteria identification and characterization of a conserved phosphoheptose isomerase." Brooke J.S., Valvano M.A. J. Biol. Chem. 271:3608-3614(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"dinP, a new gene in Escherichia coli, whose product shows similarities to UmuC and its homologues." Ohmori H., Hatada E., Qiao Y., Tsuji M., Fukuda R. Mutat. Res. 347:1-7(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"Systematic sequencing of the Escherichia coli genome: analysis of the 4.0 - 6.0 min (189,987 - 281,416bp) region." Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T., Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S., Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K. Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"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.
[6]	"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.
[7]	"Biosynthesis pathway of ADP-L-glycero-beta-D-manno-heptose in Escherichia coli." Kneidinger B., Marolda C., Graninger M., Zamyatina A., McArthur F., Kosma P., Valvano M.A., Messner P. J. Bacteriol. 184:363-369(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, ADP-L-GLYCERO-BETA-D-MANNO-HEPTOSE BIOSYNTHESIS PATHWAY. Strain: K12 / DH5-alpha and K12 / MG1655 / ATCC 47076.
[8]	"Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides." Valvano M.A., Messner P., Kosma P. Microbiology 148:1979-1989(2002) [PubMed] [Europe PMC] [Abstract] Cited for: BIOSYNTHESIS OF NUCLEOTIDE-ACTIVATED GLYCERO-MANNO-HEPTOSE.
[9]	"Lipopolysaccharide endotoxins." Raetz C.R.H., Whitfield C. Annu. Rev. Biochem. 71:635-700(2002) [PubMed] [Europe PMC] [Abstract] Cited for: LIPOPOLYSACCHARIDE REVIEW.
[10]	"Structure and function of sedoheptulose-7-phosphate isomerase, a critical enzyme for lipopolysaccharide biosynthesis and a target for antibiotic adjuvants." Taylor P.L., Blakely K.M., de Leon G.P., Walker J.R., McArthur F., Evdokimova E., Zhang K., Valvano M.A., Wright G.D., Junop M.S. J. Biol. Chem. 283:2835-2845(2008) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH SEDOHEPTULOSE-7-PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF HIS-61; GLU-65; ARG-69; ASP-94; THR-120; ASP-169; GLN-172 AND HIS-180.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U32590 Genomic DNA. Translation: AAC43630.1.
D38582 Genomic DNA. Translation: BAA07584.1.
U70214 Genomic DNA. Translation: AAB08644.1. Different initiation.
U00096 Genomic DNA. Translation: AAC73326.1.
AP009048 Genomic DNA. Translation: BAA77892.1.

PIR

G64746.

RefSeq

NP_414757.1. NC_000913.2.
YP_488519.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2I22	X-ray	2.80	A/B/C/D	1-192	[»]
2I2W	X-ray	1.95	A/B/C/D	1-192	[»]

ProteinModelPortal

P63224.

SMR

P63224. Positions 1-192.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48179N.

STRING

511145.b0222.

Proteomic databases

PaxDb

P63224.

PRIDE

P63224.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73326; AAC73326; b0222.
BAA77892; BAA77892; BAA77892.

GeneID

12934376.
949134.

KEGG

ecj:Y75_p0213.
eco:b0222.

PATRIC

32115559. VBIEscCol129921_0224.

Organism-specific databases

EchoBASE

EB2940.

EcoGene

EG13146. gmhA.

Phylogenomic databases

eggNOG

COG0279.

HOGENOM

HOG000237571.

KO

K03271.

OMA

FLAHKEA.

ProtClustDB

PRK00414.

Enzyme and pathway databases

BioCyc

EcoCyc:G6106-MONOMER.
ECOL316407:JW0212-MONOMER.
MetaCyc:G6106-MONOMER.

UniPathway

UPA00041; UER00436.
UPA00958.

Gene expression databases

Genevestigator

P63224.

Family and domain databases

HAMAP

MF_00067. GmhA.

InterPro

IPR004515. Phosphoheptose_Isoase.
IPR001347. SIS.
[Graphical view]

Pfam

PF13580. SIS_2. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00441. gmhA. 1 hit.

PROSITE

PS51464. SIS. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P63224.

Entry information

Entry name

GMHA_ECOLI

Accession

Primary (citable) accession number: P63224
Secondary accession number(s): P51001

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 27, 2004
Last sequence update:	September 27, 2004
Last modified:	May 1, 2013
This is version 77 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program