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B3DUG9

- DEF_METI4

UniProt

B3DUG9 - DEF_METI4

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Protein

Peptide deformylase

Gene
def, Minf_0917
Organism
Methylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain V4))
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 bindingi106 – 1061Iron By similarity
Metal bindingi148 – 1481Iron By similarity
Active sitei149 – 1491 By similarity
Metal bindingi152 – 1521Iron By similarity

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

BioCyciMINF481448:GJEI-932-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:Minf_0917
OrganismiMethylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain V4))
Taxonomic identifieri481448 [NCBI]
Taxonomic lineageiBacteriaVerrucomicrobiaunclassified VerrucomicrobiaMethylacidiphilalesMethylacidiphilaceaeMethylacidiphilum
ProteomesiUP000009149: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 190190Peptide deformylaseUniRule annotationPRO_1000097323Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi481448.Minf_0917.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiTFIDNMF.
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.

B3DUG9-1 [UniParc]FASTAAdd to Basket

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MILKLVLYDN PILRKKGMPI DSFDDRLKRL VQDMLETMAY YKGVGLAAQQ    50
VGLNLQLAVI DVSGSKLSSS LLIGGKPAMV EEHMPLFLIN PTLSYTQSKE 100
ISNEGCLSFP GLRIDVPRSK RVKVKTFDLE GRPWYFEAGG FLSVAIQHEF 150
DHLQGKLFID YLSAEQKKAI KEELEKIKRG EAILSVKETD 190
Length:190
Mass (Da):21,388
Last modified:July 22, 2008 - v1
Checksum:i486AC49046D19A82
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000975 Genomic DNA. Translation: ACD82972.1.
RefSeqiYP_001939570.1. NC_010794.1.

Genome annotation databases

EnsemblBacteriaiACD82972; ACD82972; Minf_0917.
GeneIDi6351842.
KEGGimin:Minf_0917.
PATRICi22490949. VBIMetInf111569_0970.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000975 Genomic DNA. Translation: ACD82972.1 .
RefSeqi YP_001939570.1. NC_010794.1.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 481448.Minf_0917.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACD82972 ; ACD82972 ; Minf_0917 .
GeneIDi 6351842.
KEGGi min:Minf_0917.
PATRICi 22490949. VBIMetInf111569_0970.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyci MINF481448:GJEI-932-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 the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia."
    Hou S., Makarova K.S., Saw J.H., Senin P., Ly B.V., Zhou Z., Ren Y., Wang J., Galperin M.Y., Omelchenko M.V., Wolf Y.I., Yutin N., Koonin E.V., Stott M.B., Mountain B.W., Crowe M.A., Smirnova A.V., Dunfield P.F.
    , Feng L., Wang L., Alam M.
    Biol. Direct 3:26-26(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Isolate V4.

Entry informationi

Entry nameiDEF_METI4
AccessioniPrimary (citable) accession number: B3DUG9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 22, 2008
Last modified: February 19, 2014
This is version 39 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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