P24197 (YGID_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Uncharacterized protein ygiD
EC=1.13.-.-

Gene names

Name:	ygiD
Ordered Locus Names:	b3039, JW3007

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	262 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Cofactor	Binds 1 zinc ion per subunit.
Sequence similarities	Belongs to the DODA-type extradiol aromatic ring-opening dioxygenase family.
Sequence caution	The sequence AAA69207.1 differs from that shown. Reason: Erroneous initiation. The sequence AAA71877.1 differs from that shown. Reason: Erroneous initiation. The sequence BAE77095.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Ligand	Metal-binding Zinc
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	cellular aromatic compound metabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	ferrous iron binding Inferred from electronic annotation. Source: InterPro oxidoreductase activity, acting on single donors with incorporation of molecular oxygen Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 262

262

Uncharacterized protein ygiD

PRO_0000169405

Sites

Metal binding

13

1

Zinc

Metal binding

48

1

Zinc

Metal binding

168

1

Zinc

Metal binding

225

1

Zinc

Experimental info

Sequence conflict

234 – 261

28

GAWDG…LSVQI → RYVGWAGANYHS in AAA71877. Ref.1

Secondary structure

1

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262

Helix Strand Turn

Details...

Beta strand

8 – 12

5

Helix

24 – 35

12

Beta strand

40 – 57

18

Helix

86 – 96

11

Beta strand

101 – 106

6

Helix

112 – 121

10

Beta strand

129 – 135

7

Helix

140 – 150

11

Helix

151 – 156

6

Beta strand

158 – 164

7

Beta strand

175 – 177

3

Helix

183 – 193

11

Turn

194 – 197

4

Helix

202 – 204

3

Turn

206 – 208

3

Helix

210 – 212

3

Helix

216 – 219

4

Beta strand

221 – 223

3

Turn

224 – 226

3

Helix

227 – 234

8

Beta strand

238 – 240

3

Turn

251 – 253

3

Beta strand

259 – 261

3

Sequences

	Sequence		Length	Mass (Da)
	P24197 [UniParc]. Last modified November 24, 2009. Version 3. Checksum: 7CFF9150AD49D50C	FASTA	262	28,892
	10 20 30 40 50 60 MSSTRMPALF LGHGSPMNVL EDNLYTRSWQ KLGMTLPRPQ AIVVVSAHWF TRGTGVTAME 70 80 90 100 110 120 TPPTIHDFGG FPQALYDTHY PAPGSPALAQ RLVELLAPIP VTLDKEAWGF DHGSWGVLIK 130 140 150 160 170 180 MYPDADIPMV QLSIDSSKPA AWHFEMGRKL AALRDEGIML VASGNVVHNL RTVKWHGDSS 190 200 210 220 230 240 PYPWATSFNE YVKANLTWQG PVEQHPLVNY LDHEGGTLSN PTPEHYLPLL YVLGAWDGQE 250 260 PITIPVEGIE MGSLSMLSVQ IG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of a region duplicated in Escherichia coli toc mutants." Yang T.-P., Depew R.E. Biochim. Biophys. Acta 1130:227-228(1992) [PubMed: 1314093] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"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.
[3]	"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.
[4]	"Crystal structure of uncharacterized protein JW3007 from Escherichia coli K12." Southeast collaboratory for structural genomics (SECSG) Submitted (JUN-2007) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS), ZINC BINDING.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M77129 Genomic DNA. Translation: AAA71877.1. Different initiation.
U28377 Genomic DNA. Translation: AAA69207.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76075.2.
AP009048 Genomic DNA. Translation: BAE77095.1. Different initiation.

PIR

E65091.

RefSeq

NP_417511.2. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2PW6	X-ray	2.27	A	1-262	[»]

ProteinModelPortal

P24197.

SMR

P24197. Positions 5-262.

ModBase

Search...

Protein-protein interaction databases

IntAct

P24197. 3 interactions.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000003484; EBESCP00000003484; EBESCG00000002859.
EBESCT00000018331; EBESCP00000017622; EBESCG00000017385.

GeneID

946447.

GenomeReviews

Gene locus JW3007 in contig AP009048_GR.
Gene locus b3039 in contig U00096_GR.

KEGG

ecj:JW3007.
eco:b3039.

PATRIC

32121488. VBIEscCol129921_3131.

Organism-specific databases

EchoBASE

EB1154.

EcoGene

EG11166. ygiD.

Phylogenomic databases

eggNOG

COG3384.

GeneTree

EBGT00050000011581.

HOGENOM

HBG313712.

PhylomeDB

P24197.

ProtClustDB

PRK10628.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11166-MONOMER.

Gene expression databases

Genevestigator

P24197.

Family and domain databases

InterPro

IPR014436. Extradiol_dOase_DODA.
IPR004183. Xdiol_dOase_suB.
[Graphical view]

Gene3D

G3DSA:3.40.830.10. Xdiol_dOase_3B. 1 hit.

Pfam

PF02900. LigB. 1 hit.
[Graphical view]

PIRSF

PIRSF006157. Doxgns_DODA. 1 hit.

SUPFAM

SSF53213. Xdiol_dOase_3B. 1 hit.

ProtoNet

Search...

Entry information

Entry name

YGID_ECOLI

Accession

Primary (citable) accession number: P24197
Secondary accession number(s): Q2M9G1

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 1992
Last sequence update:	November 24, 2009
Last modified:	January 25, 2012
This is version 88 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program