Reviewed, UniProtKB/Swiss-Prot Q9KVU3 (DEF1_VIBCH)

Names and origin

Protein names

Recommended name:
    Peptide deformylase 1
      Short name=PDF 1
    EC=3.5.1.88
Alternative name(s):
    Polypeptide deformylase 1

Gene names

Name:	def1
Ordered Locus Names:	VC_0046

Organism

Vibrio cholerae [Complete proteome] [HAMAP]

Taxonomic identifier

666 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length	169 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
Cofactor	Binds 1 Fe2+ ion By similarity. HAMAP MF_00163
Sequence similarities	Belongs to the polypeptide deformylase family.

Ontologies

Keywords
Biological process	Protein biosynthesis
Ligand	Iron Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	translation Inferred from electronic annotation. Source: HAMAP
Molecular function	iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW 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

Molecule processing

Chain

1 – 169

169

Peptide deformylase 1 HAMAP MF_00163

PRO_0000082873

Sites

Active site

134

1

By similarity

Metal binding

91

1

Iron By similarity

Metal binding

133

1

Iron By similarity

Metal binding

137

1

Iron By similarity

Secondary structure

1

.

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.

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169

Helix Strand Turn

Details...

Helix

12 – 15

4

Helix

26 – 41

16

Helix

49 – 52

4

Beta strand

56 – 61

6

Beta strand

71 – 82

12

Beta strand

87 – 89

3

Beta strand

99 – 112

14

Beta strand

118 – 123

6

Helix

125 – 138

14

Helix

143 – 146

4

Helix

149 – 163

15

Sequences

	Sequence		Length	Mass (Da)
	Q9KVU3-1 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: 16DB00B08CA40FC7	FASTA	169	19,147
	10 20 30 40 50 60 MSVLQVLTFP DDRLRTVAKP VEQVTPEIQQ IVDDMLETMY AEEGIGLAAT QVDIHQRIVV 70 80 90 100 110 120 IDISETRDQP MVLINPEIIE KRGEDGIEEG CLSVPGARAL VPRAAEVTVK ALDRNGQEYQ 130 140 150 160 FDADDLLAIC VQHELDHLAG KLFVDYLSPL KRNRIKEKLE KIKRFNEKK

References

[1]

"DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae." Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L., Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R., Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D., Vamathevan J.J., Bass S. , Qin H., Dragoi I., Sellers P., McDonald L.A., Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L., Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M. Nature 406:477-483(2000) [PubMed: 10952301] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 39315 / El Tor Inaba N16961 / Serotype O1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE003852 Genomic DNA. Translation: AAF93224.1.

PIR

A82373.

RefSeq

NP_229705.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3FWX	X-ray	2.00	A/B	1-169	[»]

ModBase

Search...

Genome annotation databases

GeneID

2614445.

GenomeReviews

Gene locus VC_0046 in contig AE003852_GR.

KEGG

vch:VC0046.

TIGR

VC_0046.

Phylogenomic databases

HOGENOM

HBG665227.

OMA

RQLVDDM.

Enzyme and pathway databases

BRENDA

3.5.1.88. 19019.

Family and domain databases

HAMAP

MF_00163. Pep_deformylase.
[Tree]

InterPro

IPR000181. Fmet_deformylase.
[Graphical view]

Gene3D

G3DSA:3.90.45.10. Fmet_deformylase. 1 hit.

PANTHER

PTHR10458. Fmet_deformylase. 1 hit.

Pfam

PF01327. Pep_deformylase. 1 hit.
[Graphical view]

PIRSF

PIRSF004749. Pep_def. 1 hit.

PRINTS

PR01576. PDEFORMYLASE.

TIGRFAMs

TIGR00079. pept_deformyl. 1 hit.

ProtoNet

Search...

Entry information

Entry name

DEF1_VIBCH

Accession

Primary (citable) accession number: Q9KVU3

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 5, 2001
Last sequence update:	October 1, 2000
Last modified:	February 9, 2010
This is version 58 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)