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Q1CCX6

- DEF_YERPN

UniProt

Q1CCX6 - DEF_YERPN

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Protein
Peptide deformylase
Gene
def, YPN_3827, YP516_4349
Organism
Yersinia pestis bv. Antiqua (strain Nepal516)
Status
Reviewed - Annotation score: 2 out of 5 - Protein inferred from homologyi

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. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: UniProtKB-HAMAP
Complete GO annotation...

GO - Biological processi

  1. 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

BioCyciYPES377628:GIXK-3928-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase (EC:3.5.1.88)
Short name:
PDF
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:def
Ordered Locus Names:YPN_3827
ORF Names:YP516_4349
OrganismiYersinia pestis bv. Antiqua (strain Nepal516)
Taxonomic identifieri377628 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
ProteomesiUP000008936: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 170170Peptide deformylaseUniRule annotation
PRO_0000301128Add
BLAST

Proteomic databases

PRIDEiQ1CCX6.

Interactioni

Protein-protein interaction databases

STRINGi377628.YPN_3827.

Structurei

3D structure databases

ProteinModelPortaliQ1CCX6.
SMRiQ1CCX6. Positions 2-169.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiELLAICI.
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.

Q1CCX6-1 [UniParc]FASTAAdd to Basket

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MSVLQVLHYP DERLRKIAAP VKEVNGEIQR IVDDMFETMY AEEGIGLAAT    50
QVDVHQQIIV IDISENRDQR LVLINPELLE KSGETGIEEG CLSIPEQRAL 100
VPRAEKVKIR ALDRDGKPFE LETDGLLAIC IQHEMDHLIG KLFVDYLSPL 150
KRQRIRQKLE KMAKLNARAN 170
Length:170
Mass (Da):19,391
Last modified:July 11, 2006 - v1
Checksum:iEB01048E0E2423A7
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000305 Genomic DNA. Translation: ABG20154.1.
ACNQ01000019 Genomic DNA. Translation: EEO74741.1.
RefSeqiYP_649754.1. NC_008149.1.

Genome annotation databases

EnsemblBacteriaiABG20154; ABG20154; YPN_3827.
EEO74741; EEO74741; YP516_4349.
GeneIDi4123298.
KEGGiypn:YPN_3827.
PATRICi18607781. VBIYerPes46733_4518.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000305 Genomic DNA. Translation: ABG20154.1 .
ACNQ01000019 Genomic DNA. Translation: EEO74741.1 .
RefSeqi YP_649754.1. NC_008149.1.

3D structure databases

ProteinModelPortali Q1CCX6.
SMRi Q1CCX6. Positions 2-169.
ModBasei Search...

Protein-protein interaction databases

STRINGi 377628.YPN_3827.

Proteomic databases

PRIDEi Q1CCX6.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABG20154 ; ABG20154 ; YPN_3827 .
EEO74741 ; EEO74741 ; YP516_4349 .
GeneIDi 4123298.
KEGGi ypn:YPN_3827.
PATRICi 18607781. VBIYerPes46733_4518.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243509.
KOi K01462.
OMAi ELLAICI.
OrthoDBi EOG664CMF.

Enzyme and pathway databases

BioCyci YPES377628:GIXK-3928-MONOMER.

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. "Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen."
    Chain P.S.G., Hu P., Malfatti S.A., Radnedge L., Larimer F., Vergez L.M., Worsham P., Chu M.C., Andersen G.L.
    J. Bacteriol. 188:4453-4463(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Nepal516.
  2. "Yersinia pestis Nepal516A whole genome shotgun sequencing project."
    Plunkett G. III, Anderson B.D., Baumler D.J., Burland V., Cabot E.L., Glasner J.D., Mau B., Neeno-Eckwall E., Perna N.T., Munk A.C., Tapia R., Green L.D., Rogers Y.C., Detter J.C., Bruce D.C., Brettin T.S.
    Submitted (APR-2009) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiDEF_YERPN
AccessioniPrimary (citable) accession number: Q1CCX6
Secondary accession number(s): D1Q2I8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: July 11, 2006
Last modified: May 14, 2014
This is version 59 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

Complete proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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