Reviewed, UniProtKB/Swiss-Prot P31545 (YCDB_ECOLI)

Names and origin

Protein names

Recommended name:
    Peroxidase ycdB
    EC=1.11.1.-

Gene names

Name:	ycdB
Ordered Locus Names:	b1019, JW1004

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	423 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	May have a role as a peroxidase under acidic conditions. Ref.5
Cofactor	Binds 1 heme B (iron-protoporphyrin IX) group non-covalently. Ref.5
Subunit structure	Homodimer. Ref.5
Subcellular location	Periplasm Ref.5.
Post-translational modification	Exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven. Can also be exported by the Sec system.
Sequence similarities	Belongs to the DyP-type peroxidase family.
Mass spectrometry	Molecular mass is 43814 Da from positions 36 - 423. Determined by ESI. Ref.5

Ontologies

Keywords
Cellular component	Periplasm
Domain	Signal
Ligand	Heme Iron Metal-binding
Molecular function	Oxidoreductase Peroxidase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	ferrous iron transport Inferred from genetic interaction. Source: UniProtKB iron assimilation Inferred from mutant phenotype. Source: UniProtKB oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from genetic interaction. Source: UniProtKB periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW oxidoreductase activity, acting on heme group of donors Ref.5 Inferred from direct assay. Source: UniProtKB peroxidase 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
	Signal peptide	1 – 35	35	Tat-type signal Probable
	Chain	36 – 423	388	Peroxidase ycdB		PRO_0000013817

Sequences

	Sequence		Length	Mass (Da)
	P31545-1 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: 65D381F829DB2570	FASTA	423	46,754
	10 20 30 40 50 60 MQYKDENGVN EPSRRRLLKV IGALALAGSC PVAHAQKTQS APGTLSPDAR NEKQPFYGEH 70 80 90 100 110 120 QAGILTPQQA AMMLVAFDVL ASDKADLERL FRLLTQRFAF LTQGGAAPET PNPRLPPLDS 130 140 150 160 170 180 GILGGYIAPD NLTITLSVGH SLFDERFGLA PQMPKKLQKM TRFPNDSLDA ALCHGDVLLQ 190 200 210 220 230 240 ICANTQDTVI HALRDIIKHT PDLLSVRWKR EGFISDHAAR SKGKETPINL LGFKDGTANP 250 260 270 280 290 300 DSQNDKLMQK VVWVTADQQE PAWTIGGSYQ AVRLIQFRVE FWDRTPLKEQ QTIFGRDKQT 310 320 330 340 350 360 GAPLGMQHEH DVPDYASDPE GKVIALDSHI RLANPRTAES ESSLMLRRGY SYSLGVTNSG 370 380 390 400 410 420 QLDMGLLFVC YQHDLEKGFL TVQKRLNGEA LEEYVKPIGG GYFFALPGVK DANDYFGSAL LRV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: 8905232] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[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]	"Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli." Kim S.-K., Makino K., Amemura M., Shinagawa H., Nakata A. J. Bacteriol. 175:1316-1324(1993) [PubMed: 8444794] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 196-423. Strain: K12.
[5]	"YcdB from Escherichia coli reveals a novel class of Tat-dependently translocated hemoproteins." Sturm A., Schierhorn A., Lindenstrauss U., Lilie H., Brueser T. J. Biol. Chem. 281:13972-13978(2006) [PubMed: 16551627] [Abstract] Cited for: FUNCTION, SUBUNIT, EXPORT VIA THE TAT-SYSTEM, SUBCELLULAR LOCATION, COFACTOR, MASS SPECTROMETRY. Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[6]	"Export pathway selectivity of Escherichia coli twin arginine translocation signal peptides." Tullman-Ercek D., DeLisa M.P., Kawarasaki Y., Iranpour P., Ribnicky B., Palmer T., Georgiou G. J. Biol. Chem. 282:8309-8316(2007) [PubMed: 17218314] [Abstract] Cited for: EXPORT VIA THE TAT-SYSTEM AND THE SEC-SYSTEM.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00096 Genomic DNA. Translation: AAC74104.1. AP009048 Genomic DNA. Translation: BAA35800.1. D10391 Genomic DNA. Translation: BAA01229.1.
PIR	A64844.
RefSeq	AP_001648.1. NP_415538.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	P31545.
Protein family/group databases
PeroxiBase	5870. EcoDyPrx01_K12.
TCDB	9.A.10.2.3. iron/lead transporter (ILT) superfamily.
Genome annotation databases
GeneID	946500.
GenomeReviews	Gene locus JW1004 in contig AP009048_GR. Gene locus b1019 in contig U00096_GR.
KEGG	ecj:JW1004. eco:b1019.
Organism-specific databases
EchoBASE	EB1686.
EcoGene	EG11735. ycdB.
CMR	Search...
Phylogenomic databases
eggNOG	COG2837.
HOGENOM	HBG296848.
OMA	VERWDRT.
Enzyme and pathway databases
BioCyc	EcoCyc:EG11735-MONOMER. ECOL168927:B1019-MONOMER. MetaCyc:EG11735-MONOMER.
Gene expression databases
Genevestigator	P31545.
Family and domain databases
InterPro	IPR006314. Dyp_peroxidase. IPR006313. Tat_enzyme. IPR006311. TAT_signal. IPR017909. Twin_arg_translocation_Tat. [Graphical view]
Pfam	PF04261. Dyp_perox. 1 hit. [Graphical view]
TIGRFAMs	TIGR01413. Dyp_perox_fam. 1 hit. TIGR01409. TAT_signal_seq. 1 hit. TIGR01412. tat_substr_1. 1 hit.
PROSITE	PS51404. DYP_PEROXIDASE. 1 hit. PS51318. TAT. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

YCDB_ECOLI

Accession

Primary (citable) accession number: P31545
Secondary accession number(s): P75903

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	November 1, 1997
Last modified:	February 9, 2010
This is version 73 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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