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Q9KVU3

- DEF1_VIBCH

UniProt

Q9KVU3 - DEF1_VIBCH

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Protein

Peptide deformylase 1

Gene

def1

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.UniRule annotation

Catalytic activityi

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

Cofactori

Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi91 – 911IronUniRule annotation
Metal bindingi133 – 1331IronUniRule annotation
Active sitei134 – 1341UniRule annotation
Metal bindingi137 – 1371IronUniRule annotation

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 1UniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDF 1UniRule annotation
Alternative name(s):
Polypeptide deformylase 1UniRule annotation
Gene namesi
Name:def1UniRule annotation
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 1PRO_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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9KVU3.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

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 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSVLQVLTFP DDRLRTVAKP VEQVTPEIQQ IVDDMLETMY AEEGIGLAAT
60 70 80 90 100
QVDIHQRIVV IDISETRDQP MVLINPEIIE KRGEDGIEEG CLSVPGARAL
110 120 130 140 150
VPRAAEVTVK ALDRNGQEYQ FDADDLLAIC VQHELDHLAG KLFVDYLSPL
160
KRNRIKEKLE KIKRFNEKK
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: October 1, 2014
This is version 84 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