Reviewed, UniProtKB/Swiss-Prot Q46891 (YGBM_ECOLI)

Names and origin

Protein names

Recommended name:
    Protein ygbM

Gene names

Name:	ygbM
Ordered Locus Names:	b2739, JW2709

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	258 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Sequence similarities

Belongs to the hyi family.

Ontologies

Keywords
Ligand	Metal-binding
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Molecular function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
groL	P0A6F5	1	EBI-1130107,EBI-543750

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 258

258

Protein ygbM

PRO_0000209109

Sites

Metal binding

143

1

Divalent metal cation

Metal binding

178

1

Divalent metal cation

Metal binding

204

1

Divalent metal cation

Metal binding

240

1

Divalent metal cation

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

258

Helix Strand Turn

Details...

Beta strand

4 – 7

4

Turn

8 – 10

3

Helix

17 – 19

3

Helix

20 – 27

8

Beta strand

30 – 33

4

Helix

42 – 51

10

Beta strand

55 – 60

6

Helix

66 – 68

3

Helix

80 – 96

17

Beta strand

100 – 103

4

Helix

115 – 133

19

Helix

134 – 136

3

Beta strand

139 – 142

4

Turn

147 – 149

3

Helix

158 – 168

11

Beta strand

173 – 178

6

Helix

179 – 185

7

Helix

189 – 195

7

Turn

196 – 198

3

Beta strand

199 – 205

7

Turn

208 – 210

3

Beta strand

214 – 219

6

Helix

221 – 230

10

Beta strand

237 – 239

3

Helix

248 – 251

4

Sequences

	Sequence		Length	Mass (Da)
	Q46891-1 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 07392B724316D7DD	FASTA	258	29,217
	10 20 30 40 50 60 MPRFAANLSM MFTEVPFIER FAAARKAGFD AVEFLFPYNY STLQIQKQLE QNHLTLALFN 70 80 90 100 110 120 TAPGDINAGE WGLSALPGRE HEAHADIDLA LEYALALNCE QVHVMAGVVP AGEDAERYRA 130 140 150 160 170 180 VFIDNIRYAA DRFAPHGKRI LVEALSPGVK PHYLFSSQYQ ALAIVEEVAR DNVFIQLDTF 190 200 210 220 230 240 HAQKVDGNLT HLIRDYAGKY AHVQIAGLPD RHEPDDGEIN YPWLFRLFDE VGYQGWIGCE 250 YKPRGLTEEG LGWFDAWR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM." Kim Y., Skarina T., Beasley S., Laskowski R., Arrowsmith C., Joachimiak A., Edwards A., Savchenko A. Proteins 48:427-430(2002) [PubMed: 12112708] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.63 ANGSTROMS) IN COMPLEX WITH MAGNESIUM IONS.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U29579 Genomic DNA. Translation: AAA69249.1.
U00096 Genomic DNA. Translation: AAC75781.1.
AP009048 Genomic DNA. Translation: BAE76816.1.

PIR

G65054.

RefSeq

AP_003306.1.
NP_417219.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1K77	X-ray	1.63	A	1-258	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:12114N.

IntAct

Q46891. 1 interaction.

Genome annotation databases

GeneID

947207.

GenomeReviews

Gene locus JW2709 in contig AP009048_GR.
Gene locus b2739 in contig U00096_GR.

KEGG

ecj:JW2709.
eco:b2739.

Organism-specific databases

EchoBASE

EB2910.

EcoGene

EG13107. ygbM.

CMR

Search...

Phylogenomic databases

HOGENOM

Q46891.

OMA

Q46891. GHVQIAG.

Enzyme and pathway databases

BioCyc

EcoCyc:G7420-MON.

Family and domain databases

InterPro

IPR013022. Xyl_isomerase-like_TIM-brl.
IPR012307. Xyl_isomerase-typ_TIM-brl.
[Graphical view]

Gene3D

G3DSA:3.20.20.150. Xyl_isomerase-like_TIM-brl. 1 hit.

Pfam

PF01261. AP_endonuc_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

YGBM_ECOLI

Accession

Primary (citable) accession number: Q46891
Secondary accession number(s): Q2MA90

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	June 16, 2009
This is version 63 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)