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Protein

Peptide deformylase 2

Gene

defB

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: -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.

Catalytic activityi

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

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi110IronBy similarity1
Metal bindingi153IronBy similarity1
Active sitei154By similarity1
Metal bindingi157IronBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase
Biological processProtein biosynthesis
LigandIron, Metal-binding

Enzyme and pathway databases

BioCyciBSUB:BSU14560-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 2 (EC:3.5.1.88)
Short name:
PDF 2
Alternative name(s):
Polypeptide deformylase 2
Gene namesi
Name:defB
Synonyms:ykrB
Ordered Locus Names:BSU14560
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000827401 – 184Peptide deformylase 2Add BLAST184

Proteomic databases

PaxDbiQ45495
PRIDEiQ45495

Interactioni

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100008071

Structurei

3D structure databases

ProteinModelPortaliQ45495
SMRiQ45495
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiENOG4108Z02 Bacteria
COG0242 LUCA
HOGENOMiHOG000243507
InParanoidiQ45495
KOiK01462
OMAiMILMKDI
PhylomeDBiQ45495

Family and domain databases

CDDicd00487 Pep_deformylase, 1 hit
Gene3Di3.90.45.10, 1 hit
HAMAPiMF_00163 Pep_deformylase, 1 hit
InterProiView protein in InterPro
IPR023635 Peptide_deformylase
IPR036821 Peptide_deformylase_sf
PANTHERiPTHR10458 PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327 Pep_deformylase, 1 hit
PIRSFiPIRSF004749 Pep_def, 1 hit
PRINTSiPR01576 PDEFORMYLASE
SUPFAMiSSF56420 SSF56420, 1 hit
TIGRFAMsiTIGR00079 pept_deformyl, 1 hit

Sequencei

Sequence statusi: Complete.

Q45495-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MITMENIVRD GHPALRETAE PVELPPTDAE KQQLADMIEF VKNSQNPELA
60 70 80 90 100
EKYKLRPGVG LAAPQINIKK RMIAVHAEDA SGKLYSYALF NPKIVSHSVE
110 120 130 140 150
KSYLTSGEGC LSVDEAIPGY VPRYARIRVK GTTLEGENID IRLKGFPAIV
160 170 180
FQHEIDHLNG VMFYDHIDKE NPFKEPENAI AIER
Length:184
Mass (Da):20,656
Last modified:November 1, 1996 - v1
Checksum:i8641BF1932666C38
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF012285 Genomic DNA Translation: AAC24930.1
AL009126 Genomic DNA Translation: CAB13329.1
PIRiD69862
RefSeqiNP_389339.1, NC_000964.3
WP_003245474.1, NZ_JNCM01000035.1

Genome annotation databases

EnsemblBacteriaiCAB13329; CAB13329; BSU14560
GeneIDi939491
KEGGibsu:BSU14560
PATRICifig|224308.179.peg.1587

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF012285 Genomic DNA Translation: AAC24930.1
AL009126 Genomic DNA Translation: CAB13329.1
PIRiD69862
RefSeqiNP_389339.1, NC_000964.3
WP_003245474.1, NZ_JNCM01000035.1

3D structure databases

ProteinModelPortaliQ45495
SMRiQ45495
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100008071

Proteomic databases

PaxDbiQ45495
PRIDEiQ45495

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13329; CAB13329; BSU14560
GeneIDi939491
KEGGibsu:BSU14560
PATRICifig|224308.179.peg.1587

Phylogenomic databases

eggNOGiENOG4108Z02 Bacteria
COG0242 LUCA
HOGENOMiHOG000243507
InParanoidiQ45495
KOiK01462
OMAiMILMKDI
PhylomeDBiQ45495

Enzyme and pathway databases

BioCyciBSUB:BSU14560-MONOMER

Family and domain databases

CDDicd00487 Pep_deformylase, 1 hit
Gene3Di3.90.45.10, 1 hit
HAMAPiMF_00163 Pep_deformylase, 1 hit
InterProiView protein in InterPro
IPR023635 Peptide_deformylase
IPR036821 Peptide_deformylase_sf
PANTHERiPTHR10458 PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327 Pep_deformylase, 1 hit
PIRSFiPIRSF004749 Pep_def, 1 hit
PRINTSiPR01576 PDEFORMYLASE
SUPFAMiSSF56420 SSF56420, 1 hit
TIGRFAMsiTIGR00079 pept_deformyl, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDEF2_BACSU
AccessioniPrimary (citable) accession number: Q45495
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1996
Last modified: October 10, 2018
This is version 123 of the entry and version 1 of the sequence. See 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
  2. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
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Main funding by: National Institutes of Health

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