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Q9KVU3

- DEF1_VIBCH

UniProt

Q9KVU3 - DEF1_VIBCH

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Protein

Peptide deformylase 1

Gene
def1, VC_0046
Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

Functioni

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.UniRule annotation

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.UniRule annotation

Cofactori

Binds 1 Fe2+ ion By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi91 – 911Iron By similarity
Metal bindingi133 – 1331Iron By similarity
Active sitei134 – 1341 By similarity
Metal bindingi137 – 1371Iron By similarity

GO - Molecular functioni

  1. formylmethionine deformylase activity Source: TIGR
  2. iron ion binding Source: InterPro
  3. peptide deformylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. cellular protein modification process Source: TIGR
  2. translation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciVCHO:VC0046-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1 (EC:3.5.1.88)
Short name:
PDF 1
Alternative name(s):
Polypeptide deformylase 1
Gene namesi
Name:def1
Ordered Locus Names:VC_0046
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000000584: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 169169Peptide deformylase 1UniRule annotationPRO_0000082873Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi243277.VC0046.

Structurei

Secondary structure

1
169
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi12 – 154
Helixi26 – 4116
Beta strandi45 – 484
Helixi49 – 524
Beta strandi56 – 616
Beta strandi71 – 8313
Beta strandi85 – 895
Beta strandi99 – 1035
Beta strandi105 – 1128
Beta strandi118 – 1236
Helixi125 – 13814
Helixi143 – 1464
Helixi149 – 16315

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3FWXX-ray2.00A/B1-169[»]
ProteinModelPortaliQ9KVU3.
SMRiQ9KVU3. Positions 2-168.

Miscellaneous databases

EvolutionaryTraceiQ9KVU3.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiASHINGA.
OrthoDBiEOG664CMF.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9KVU3-1 [UniParc]FASTAAdd to Basket

« Hide

MSVLQVLTFP DDRLRTVAKP VEQVTPEIQQ IVDDMLETMY AEEGIGLAAT    50
QVDIHQRIVV IDISETRDQP MVLINPEIIE KRGEDGIEEG CLSVPGARAL 100
VPRAAEVTVK ALDRNGQEYQ FDADDLLAIC VQHELDHLAG KLFVDYLSPL 150
KRNRIKEKLE KIKRFNEKK 169
Length:169
Mass (Da):19,147
Last modified:October 1, 2000 - v1
Checksum:i16DB00B08CA40FC7
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE003852 Genomic DNA. Translation: AAF93224.1.
PIRiA82373.
RefSeqiNP_229705.1. NC_002505.1.

Genome annotation databases

EnsemblBacteriaiAAF93224; AAF93224; VC_0046.
GeneIDi2614445.
KEGGivch:VC0046.
PATRICi20079140. VBIVibCho83274_0045.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE003852 Genomic DNA. Translation: AAF93224.1 .
PIRi A82373.
RefSeqi NP_229705.1. NC_002505.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3FWX X-ray 2.00 A/B 1-169 [» ]
ProteinModelPortali Q9KVU3.
SMRi Q9KVU3. Positions 2-168.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 243277.VC0046.

Protocols and materials databases

DNASUi 2614445.
Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAF93224 ; AAF93224 ; VC_0046 .
GeneIDi 2614445.
KEGGi vch:VC0046.
PATRICi 20079140. VBIVibCho83274_0045.

Phylogenomic databases

eggNOGi COG0242.
KOi K01462.
OMAi ASHINGA.
OrthoDBi EOG664CMF.

Enzyme and pathway databases

BioCyci VCHO:VC0046-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q9KVU3.

Family and domain databases

Gene3Di 3.90.45.10. 1 hit.
HAMAPi MF_00163. Pep_deformylase.
InterProi IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view ]
PANTHERi PTHR10458. PTHR10458. 1 hit.
Pfami PF01327. Pep_deformylase. 1 hit.
[Graphical view ]
PIRSFi PIRSF004749. Pep_def. 1 hit.
PRINTSi PR01576. PDEFORMYLASE.
SUPFAMi SSF56420. SSF56420. 1 hit.
TIGRFAMsi TIGR00079. pept_deformyl. 1 hit.
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 39315 / El Tor Inaba N16961.

Entry informationi

Entry nameiDEF1_VIBCH
AccessioniPrimary (citable) accession number: Q9KVU3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: October 1, 2000
Last modified: May 14, 2014
This is version 83 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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