Peroxidase ycdB precursor - Escherichia coli (strain K12)

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P31545 (YCDB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 93. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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)

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	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Cellular component	periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	iron ion binding Inferred from electronic annotation. Source: InterPro 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

Tat-type signal Probable

Chain

36 – 423

388

Peroxidase ycdB

PRO_0000013817

Sites

Active site

235

Proton acceptor By similarity

Metal binding

329

Iron (heme proximal ligand) By similarity

Secondary structure

423

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P31545 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 65D381F829DB2570
Show »

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

« Hide

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. 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.
+	Additional computationally mapped references.

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

NP_415538.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2Y4D	X-ray	2.00	A/B	36-423	[»]
2Y4E	X-ray	2.30	A/B	36-423	[»]
2Y4F	X-ray	2.70	A/B	36-423	[»]
3O72	X-ray	1.95	A/B/C/D	36-423	[»]

ProteinModelPortal

P31545.

SMR

P31545. Positions 40-423.

ModBase

Search...

Protein-protein interaction databases

IntAct

P31545. 8 interactions.

Protein family/group databases

PeroxiBase

5870. EcoDyPrx01_K12.

TCDB

9.A.10.2.3. iron/lead transporter (ILT) superfamily.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000002777; EBESCP00000002777; EBESCG00000002266.
EBESCT00000015445; EBESCP00000014736; EBESCG00000014505.

GeneID

946500.

GenomeReviews

Gene locus JW1004 in contig AP009048_GR.
Gene locus b1019 in contig U00096_GR.

KEGG

ecj:JW1004.
eco:b1019.

PATRIC

32117271. VBIEscCol129921_1059.

Organism-specific databases

EchoBASE

EB1686.

EcoGene

EG11735. ycdB.

Phylogenomic databases

eggNOG

COG2837.

GeneTree

EBGT00050000010894.

HOGENOM

HBG296848.

OMA

VERWDRT.

PhylomeDB

P31545.

ProtClustDB

CLSK879930.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11735-MONOMER.
MetaCyc:EG11735-MONOMER.

Gene expression databases

Genevestigator

P31545.

Family and domain databases

InterPro

IPR011008. Dimeric_a/b-barrel.
IPR006314. Dyp_peroxidase.
IPR006313. Tat_enzyme.
IPR006311. TAT_signal.
[Graphical view]

K07223.

Pfam

PF04261. Dyp_perox. 1 hit.
[Graphical view]

SUPFAM

SSF54909. Dimer_A_B_barrel. 1 hit.

TIGRFAMs

TIGR01413. Dyp_perox_fam. 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:	January 25, 2012
This is version 93 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protein family/group databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents