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A4XNB3

- DEF_PSEMY

UniProt

A4XNB3 - DEF_PSEMY

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Protein

Peptide deformylase

Gene

def

Organism
Pseudomonas mendocina (strain ymp)
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.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 bindingi92 – 921IronUniRule annotation
Metal bindingi134 – 1341IronUniRule annotation
Active sitei135 – 1351UniRule annotation
Metal bindingi138 – 1381IronUniRule annotation

GO - Molecular functioni

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

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

BioCyciPMEN399739:GHR6-54-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylaseUniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDFUniRule annotation
Alternative name(s):
Polypeptide deformylaseUniRule annotation
Gene namesi
Name:defUniRule annotation
Ordered Locus Names:Pmen_0055
OrganismiPseudomonas mendocina (strain ymp)
Taxonomic identifieri399739 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
ProteomesiUP000000229: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 168168Peptide deformylasePRO_1000023132Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi399739.Pmen_0055.

Structurei

3D structure databases

ProteinModelPortaliA4XNB3.
SMRiA4XNB3. Positions 1-167.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiDMYDTMD.
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.

A4XNB3-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAILNILEFP DPRLRTIAKP VDVVDDSIRQ LVDDMFETMY DAPGIGLAAT
60 70 80 90 100
QVNVHKRVVV MDLSEDKSEP RVFINPEFES LTDEMDQYQE GCLSVPGFYE
110 120 130 140 150
NVDRPQKVKI KALDRDGQPF ELIAEGLLAV CIQHECDHLN GKLFVDYLSN
160
LKRDRIKKKL EKQHRQRA
Length:168
Mass (Da):19,326
Last modified:May 29, 2007 - v1
Checksum:i57444DC876B39BF4
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000680 Genomic DNA. Translation: ABP82829.1.
RefSeqiYP_001185561.1. NC_009439.1.

Genome annotation databases

EnsemblBacteriaiABP82829; ABP82829; Pmen_0055.
GeneIDi5106240.
KEGGipmy:Pmen_0055.
PATRICi19906507. VBIPseMen131592_0054.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000680 Genomic DNA. Translation: ABP82829.1 .
RefSeqi YP_001185561.1. NC_009439.1.

3D structure databases

ProteinModelPortali A4XNB3.
SMRi A4XNB3. Positions 1-167.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 399739.Pmen_0055.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABP82829 ; ABP82829 ; Pmen_0055 .
GeneIDi 5106240.
KEGGi pmy:Pmen_0055.
PATRICi 19906507. VBIPseMen131592_0054.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyci PMEN399739:GHR6-54-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ymp.

Entry informationi

Entry nameiDEF_PSEMY
AccessioniPrimary (citable) accession number: A4XNB3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 29, 2007
Last modified: October 1, 2014
This is version 48 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, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3