P0A759 (NAGB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glucosamine-6-phosphate deaminase
EC=3.5.99.6

Alternative name(s):
GlcN6P deaminase
Short name=GNPDA
Glucosamine-6-phosphate isomerase

Gene names

Name:	nagB
Synonyms:	glmD
Ordered Locus Names:	b0678, JW0664

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

General annotation (Comments)

Function	Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion. HAMAP-Rule MF_01241
Catalytic activity	D-glucosamine 6-phosphate + H2O = D-fructose 6-phosphate + NH3. HAMAP-Rule MF_01241
Enzyme regulation	Allosterically activated by N-acetylglucosamine 6-phosphate (GlcNAc6P). Competitively inhibited by 2-amino-2-deoxy-D-glucitol-6-phosphate (GlcN-ol-6P). HAMAP-Rule MF_01241
Pathway	Amino-sugar metabolism; N-acetylneuraminate degradation; D-fructose 6-phosphate from N-acetylneuraminate: step 5/5. HAMAP-Rule MF_01241
Subunit structure	Homohexamer; trimer of disulfide-linked dimers. Ref.7
Miscellaneous	Disulfide bonds seem not to be essential for the stability of the oligomer under physiological conditions. HAMAP-Rule MF_01241
Sequence similarities	Belongs to the glucosamine/galactosamine-6-phosphate isomerase family. NagB subfamily.

Ontologies

Keywords
Biological process	Carbohydrate metabolism
Molecular function	Hydrolase
PTM	Disulfide bond
Technical term	3D-structure Allosteric enzyme Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	N-acetylglucosamine catabolic process Inferred from mutant phenotype PubMed 4563983. Source: EcoCyc N-acetylneuraminate catabolic process Inferred from electronic annotation. Source: UniProtKB-UniPathway UDP-N-acetylglucosamine biosynthetic process Inferred from genetic interaction PubMed 2687246. Source: EcoCyc carbohydrate metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	glucosamine-6-phosphate deaminase activity Inferred from direct assay Ref.6. Source: EcoCyc hydrolase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 266

266

Glucosamine-6-phosphate deaminase HAMAP-Rule MF_01241

PRO_0000160143

Sites

Active site

72

1

Proton acceptor; for enolization step Ref.8

Active site

141

1

For ring-opening step Ref.8

Active site

143

1

Proton acceptor; for ring-opening step Ref.8

Active site

148

1

For ring-opening step Ref.8

Site

151

1

Part of the allosteric site

Site

158

1

Part of the allosteric site

Site

160

1

Part of the allosteric site

Site

161

1

Part of the allosteric site

Site

254

1

Part of the allosteric site

Amino acid modifications

Disulfide bond

219

Interchain Ref.7

Experimental info

Mutagenesis

118

1

C → S: 50% of wild-type activity, but 2-fold decrease in substrate affinity. Ref.6

Mutagenesis

141

1

D → N: Large decrease in activity. Ref.8

Mutagenesis

143

1

H → Q: Loss of activity for the deamination reaction but not for the reverse reaction; complete loss of the homotropic cooperativity. Ref.8

Mutagenesis

148

1

E → Q: Large decrease in activity. Ref.8

Mutagenesis

174

1

F → A: Loss of activity in the absence of the allosteric activator.

Mutagenesis

239

1

C → S: 50% of wild-type activity, but 2-fold decrease in substrate affinity; decrease in allosteric interaction energy. Ref.6

Sequence conflict

70

1

N → NM in AAC09324. Ref.2

Sequence conflict

91

1

Missing in AAC09324. Ref.2

Secondary structure

1

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266

Helix Strand Turn

Details...

Beta strand

2 – 5

4

Helix

9 – 27

19

Beta strand

31 – 33

3

Beta strand

35 – 39

5

Helix

46 – 57

12

Beta strand

66 – 76

11

Helix

85 – 92

8

Helix

94 – 96

3

Helix

101 – 103

3

Helix

114 – 128

15

Beta strand

132 – 136

5

Beta strand

157 – 161

5

Helix

164 – 170

7

Helix

171 – 173

3

Turn

174 – 176

3

Helix

178 – 180

3

Beta strand

183 – 187

5

Helix

190 – 194

5

Beta strand

199 – 203

5

Helix

206 – 208

3

Helix

209 – 217

9

Beta strand

222 – 224

3

Helix

225 – 231

7

Beta strand

233 – 239

7

Helix

242 – 244

3

Helix

249 – 263

15

Sequences

	Sequence		Length	Mass (Da)
	P0A759 [UniParc]. Last modified June 7, 2005. Version 1. Checksum: D1443A40E74AC08E	FASTA	266	29,774
	10 20 30 40 50 60 MRLIPLTTAE QVGKWAARHI VNRINAFKPT ADRPFVLGLP TGGTPMTTYK ALVEMHKAGQ 70 80 90 100 110 120 VSFKHVVTFN MDEYVGLPKE HPESYYSFMH RNFFDHVDIP AENINLLNGN APDIDAECRQ 130 140 150 160 170 180 YEEKIRSYGK IHLFMGGVGN DGHIAFNEPA SSLASRTRIK TLTHDTRVAN SRFFDNDVNQ 190 200 210 220 230 240 VPKYALTVGV GTLLDAEEVM ILVLGSQKAL ALQAAVEGCV NHMWTISCLQ LHPKAIMVCD 250 260 EPSTMELKVK TLRYFNELEA ENIKGL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequences of the Escherichia coli nagE and nagB genes: the structural genes for the N-acetylglucosamine transport protein of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and for glucosamine-6-phosphate deaminase." Rogers M.J., Ohgi T., Plumbridge J., Soell D. Gene 62:197-207(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Cloning and characterization of the N-acetylglucosamine operon of Escherichia coli." Peri K.G., Goldie H., Waygood E.B. Biochem. Cell Biol. 68:123-137(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(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]	"Identification of two cysteine residues forming a pair of vicinal thiols in glucosamine-6-phosphate deaminase from Escherichia coli and a study of their functional role by site-directed mutagenesis." Altamirano M.M., Plumbridge J.A., Calcagno M.L. Biochemistry 31:1153-1158(1992) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF CYS-118 AND CYS-239.
[7]	"Glucosamine-6-phosphate deaminase from Escherichia coli has a trimer of dimers structure with three intersubunit disulphides." Altamirano M.M., Plumbridge J.A., Barba H.A., Calcagno M.L. Biochem. J. 295:645-648(1993) [PubMed] [Europe PMC] [Abstract] Cited for: DISULFIDE BONDS.
[8]	"On the multiple functional roles of the active site histidine in catalysis and allosteric regulation of Escherichia coli glucosamine 6-phosphate deaminase." Montero-Moran G.M., Lara-Gonzalez S., Alvarez-Anorve L.I., Plumbridge J.A., Calcagno M.L. Biochemistry 40:10187-10196(2001) [PubMed] [Europe PMC] [Abstract] Cited for: ACTIVE SITES, MUTAGENESIS OF ASP-141; HIS-143 AND GLU-148.
[9]	"Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1-A resolution." Oliva G., Fontes M.R.M., Garratt R.C., Altamirano M.M., Calcagno M.L., Horjales E. Structure 3:1323-1332(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEX WITH THE INHIBITOR 2-AMINO-2-DEOXY-D-GLUCITOL-6-PHOSPHATE.
[10]	"The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3-A resolution." Horjales E., Altamirano M.M., Calcagno M.L., Garratt R.C., Oliva G. Structure 7:527-537(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[11]	"Structural flexibility, an essential component of the allosteric activation in Escherichia coli glucosamine-6-phosphate deaminase." Rudino-Pinera E., Morales-Arrieta S., Rojas-Trejo S.P., Horjales E. Acta Crystallogr. D 58:10-20(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEXES WITH FRUCTOSE-6-PHOSPHATE AND N-ACETYLGLUCOSAMINE-6-PHOSPHATE.
[12]	"On the role of the conformational flexibility of the active-site lid on the allosteric kinetics of glucosamine-6-phosphate deaminase." Bustos-Jaimes I., Sosa-Peinado A., Rudino-Pinera E., Horjales E., Calcagno M.L. J. Mol. Biol. 319:183-189(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.02 ANGSTROMS) OF MUTANT ALA-174.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M19284 Genomic DNA. Translation: AAA24191.1.
AF052007 Genomic DNA. Translation: AAC09324.1.
U00096 Genomic DNA. Translation: AAC73772.1.
AP009048 Genomic DNA. Translation: BAA35321.1.

PIR

MUECNG. A29895.

RefSeq

NP_415204.1. NC_000913.2.
YP_488958.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CD5	X-ray	2.30	A	1-266	[»]
1DEA	X-ray	2.10	A/B	1-266	[»]
1FQO	X-ray	2.20	A/B	1-266	[»]
1FRZ	X-ray	2.20	A/B	1-266	[»]
1FS5	X-ray	1.73	A/B	1-266	[»]
1FS6	X-ray	2.20	A	1-266	[»]
1FSF	X-ray	1.90	A	1-266	[»]
1HOR	X-ray	2.40	A/B	1-266	[»]
1HOT	X-ray	2.40	A/B	1-266	[»]
1JT9	X-ray	2.06	A	1-266	[»]
2WU1	X-ray	2.20	A/B	1-266	[»]

ProteinModelPortal

P0A759.

SMR

P0A759. Positions 1-266.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35992N.

IntAct

P0A759. 11 interactions.

STRING

511145.b0678.

Proteomic databases

PaxDb

P0A759.

PRIDE

P0A759.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73772; AAC73772; b0678.
BAA35321; BAA35321; BAA35321.

GeneID

12932798.
945290.

KEGG

ecj:Y75_p0657.
eco:b0678.

PATRIC

32116541. VBIEscCol129921_0703.

Organism-specific databases

EchoBASE

EB0627.

EcoGene

EG10633. nagB.

Phylogenomic databases

eggNOG

COG0363.

HOGENOM

HOG000064979.

KO

K02564.

OMA

NDFKPTA.

ProtClustDB

PRK00443.

Enzyme and pathway databases

BioCyc

EcoCyc:GLUCOSAMINE-6-P-DEAMIN-MONOMER.
ECOL316407:JW0664-MONOMER.
MetaCyc:GLUCOSAMINE-6-P-DEAMIN-MONOMER.

SABIO-RK

P0A759.

UniPathway

UPA00629; UER00684.

Gene expression databases

Genevestigator

P0A759.

Family and domain databases

HAMAP

MF_01241. GlcN6P_deamin.

InterPro

IPR006148. Glc/Gal-6P_isomerase.
IPR004547. Glucosamine6P_isomerase.
IPR018321. Glucosamine6P_isomerase_CS.
[Graphical view]

PANTHER

PTHR11280. PTHR11280. 1 hit.

Pfam

PF01182. Glucosamine_iso. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00502. nagB. 1 hit.

PROSITE

PS01161. GLC_GALNAC_ISOMERASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0A759.

Entry information

Entry name

NAGB_ECOLI

Accession

Primary (citable) accession number: P0A759
Secondary accession number(s): O68603, P09375

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	June 7, 2005
Last modified:	May 1, 2013
This is version 78 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program