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Protein

Peptide deformylase

Gene

def

Organism
Caulobacter crescentus (strain NA1000 / CB15N)
Status
Reviewed-Annotation score: 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

Fe2+UniRule annotationNote: Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi98 – 981IronUniRule annotation
Metal bindingi140 – 1401IronUniRule annotation
Active sitei141 – 1411UniRule annotation
Metal bindingi144 – 1441IronUniRule 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

BioCyciCAULONA1000:CCNA_00273-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:CCNA_00273
OrganismiCaulobacter crescentus (strain NA1000 / CB15N)
Taxonomic identifieri565050 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaeCaulobacter
ProteomesiUP000001364 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 173173Peptide deformylasePRO_1000200719Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi190650.CC_0272.

Structurei

3D structure databases

ProteinModelPortaliB8GYE3.
SMRiB8GYE3. Positions 18-171.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
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.

B8GYE3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIRRILTVD NAADLATLKK ISTPVEAVTD ELRALMDDML ETMYDAPGIG
60 70 80 90 100
LAAVQVGEPV RVIVMDLARE GEDKAPRYFV NPEILASSED LQGYEEGCLS
110 120 130 140 150
VPEYYDEVER PSKVTLRYMN YQGETVVEEA EGLFAVCIQH EMDHLEGVLF
160 170
IDHLSRLRRD RAMAKVKKAR RAA
Length:173
Mass (Da):19,445
Last modified:March 3, 2009 - v1
Checksum:i7BE0E9341CF9195F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001340 Genomic DNA. Translation: ACL93740.1.
RefSeqiWP_010918161.1. NC_011916.1.
YP_002515648.1. NC_011916.1.

Genome annotation databases

EnsemblBacteriaiACL93740; ACL93740; CCNA_00273.
GeneIDi7330726.
KEGGiccs:CCNA_00273.
PATRICi21305109. VBICauCre52860_0270.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001340 Genomic DNA. Translation: ACL93740.1.
RefSeqiWP_010918161.1. NC_011916.1.
YP_002515648.1. NC_011916.1.

3D structure databases

ProteinModelPortaliB8GYE3.
SMRiB8GYE3. Positions 18-171.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi190650.CC_0272.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL93740; ACL93740; CCNA_00273.
GeneIDi7330726.
KEGGiccs:CCNA_00273.
PATRICi21305109. VBICauCre52860_0270.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciCAULONA1000:CCNA_00273-MONOMER.

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.
ProtoNetiSearch...

Publicationsi

  1. "The genetic basis of laboratory adaptation in Caulobacter crescentus."
    Marks M.E., Castro-Rojas C.M., Teiling C., Du L., Kapatral V., Walunas T.L., Crosson S.
    J. Bacteriol. 192:3678-3688(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NA1000 / CB15N.

Entry informationi

Entry nameiDEF_CAUCN
AccessioniPrimary (citable) accession number: B8GYE3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 3, 2009
Last modified: April 1, 2015
This is version 45 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.