Peptide deformylase 2 - Xanthomonas oryzae pv. oryzae

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Q5H3Z2 (Q5H3Z2_XANOR) Unreviewed, UniProtKB/TrEMBL

Last modified December 14, 2011. Version 44. History...

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

Third-party data

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

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

Names and origin

Protein names

Recommended name:
Peptide deformylase 2 HAMAP MF_00163
Short name=PDF 2 HAMAP MF_00163
EC=3.5.1.88 HAMAP MF_00163

Alternative name(s):
Polypeptide deformylase 2 HAMAP MF_00163

Gene names

Name:	def EMBL AAW74329.1
Synonyms:	def2 HAMAP MF_00163
Ordered Locus Names:	XOO1075

Organism

Xanthomonas oryzae pv. oryzae [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Xanthomonadales › Xanthomonadaceae › Xanthomonas

Protein attributes

Sequence length	212 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions By similarity. HAMAP MF_00163
Catalytic activity	Formyl-L-methionyl peptide + H₂O = formate + methionyl peptide. HAMAP MF_00163 SAAS SAAS000181
Cofactor	Binds 1 Fe²⁺ ion By similarity. HAMAP MF_00163
Sequence similarities	Belongs to the polypeptide deformylase family. HAMAP MF_00163 RuleBase RU003335

Ontologies

Keywords
Biological process	Protein biosynthesis HAMAP MF_00163 SAAS SAAS000181
Ligand	Iron HAMAP MF_00163 Metal-binding HAMAP MF_00163 SAAS SAAS000181
Molecular function	Hydrolase HAMAP MF_00163 SAAS SAAS000181
Technical term	3D-structure PDB 3DLD Complete proteome
Gene Ontology (GO)
Biological process	translation Inferred from electronic annotation. Source: HAMAP
Molecular function	iron ion binding Inferred from electronic annotation. Source: InterPro peptide deformylase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Sites

Active site

1

By similarity HAMAP MF_00163

Metal binding

1

Iron By similarity HAMAP MF_00163

Metal binding

1

Iron By similarity HAMAP MF_00163

Metal binding

1

Iron By similarity HAMAP MF_00163

Sequences

Sequence

Length

Mass (Da)

Tools

Q5H3Z2 [UniParc].

Last modified March 1, 2005. Version 1.
Checksum: 9C1AAD3FB052C7E4
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212

23,801

        10         20         30         40         50         60 
MSVPITRSLQ FLRAVHSWLK IARLRSGSYS KLHVTIFRST PMIRDIIRMG DKRLLRVAPQ 

        70         80         90        100        110        120 
VTNLGSAELH ALVSDMFETM GAAHGVGLAA PQIAVDLQLM VFGFEASERY PEAPAVPLTA 

       130        140        150        160        170        180 
LANAQIEPLS DEMENGWEGC LSIPGLRAVI PRYRYIRYRG FAPDGSPIER EAEGFHARVV 

       190        200        210 
QHEYDHLVGR LYPSRIENFD TFGFDDVLSY DL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice." Lee B.-M., Park Y.-J., Park D.-S., Kang H.-W., Kim J.-G., Song E.-S., Park I.-C., Yoon U.-H., Hahn J.-H., Koo B.-S., Lee G.-B., Kim H., Park H.-S., Yoon K.-O., Kim J.-H., Jung C.-H., Koh N.-H., Seo J.-S., Go S.-J. Nucleic Acids Res. 33:577-586(2005) [PubMed: 15673718] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: KACC10331 / KXO85.
[2]	"Crystal structure of peptide deformylase, Xoo1075, from Xanthomonas oryzae pv. oryzae KACC10331." Ngo H.P.-T., Kim J.K., Jung J.H., Kang L.W. Submitted (JUN-2008) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 42-212.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE013598 Genomic DNA. Translation: AAW74329.1.

RefSeq

YP_199714.1. NC_006834.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3DLD	X-ray	2.60	A	42-212	[»]

ProteinModelPortal

ModBase

Protocols and materials databases

StructuralBiologyKnowledgebase

Genome annotation databases

GeneID

GenomeReviews

Gene locus XOO1075 in contig AE013598_GR.

KEGG

NMPDR

fig|291331.3.peg.1075.

PATRIC

24101118. VBIXanOry111333_1195.

Organism-specific databases

CMR

Phylogenomic databases

HOGENOM

OMA

ProtClustDB

Enzyme and pathway databases

BioCyc

XORY291331:XOO1075-MONOMER.

Family and domain databases

HAMAP

MF_00163. Pep_deformylase.
[Tree]

InterPro

IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]

Gene3D

G3DSA:3.90.45.10. Fmet_deformylase. 1 hit.

KO

PANTHER

PTHR10458. Fmet_deformylase. 1 hit.

Pfam

PF01327. Pep_deformylase. 1 hit.
[Graphical view]

PIRSF

PIRSF004749. Pep_def. 1 hit.

PRINTS

PR01576. PDEFORMYLASE.

SUPFAM

SSF56420. Fmet_deformylase. 1 hit.

TIGRFAMs

TIGR00079. Pept_deformyl. 1 hit.

ProtoNet

Entry information

Entry name

Q5H3Z2_XANOR

Accession

Primary (citable) accession number: Q5H3Z2

Entry history

Integrated into UniProtKB/TrEMBL:	March 1, 2005
Last sequence update:	March 1, 2005
Last modified:	December 14, 2011
This is version 44 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

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