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B3DUG9

- DEF_METI4

UniProt

B3DUG9 - DEF_METI4

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Protein

Peptide deformylase

Gene

def

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.UniRule annotation

Catalytic activityi

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

Cofactori

Fe2+UniRule annotationNote: Binds 1 Fe(2+) ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi106 – 1061IronUniRule annotation
Metal bindingi148 – 1481IronUniRule annotation
Active sitei149 – 1491UniRule annotation
Metal bindingi152 – 1521IronUniRule 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

BioCyciMINF481448:GJEI-932-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: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 deformylasePRO_1000097323Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi481448.Minf_0917.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

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

« Hide

        10         20         30         40         50
MILKLVLYDN PILRKKGMPI DSFDDRLKRL VQDMLETMAY YKGVGLAAQQ
60 70 80 90 100
VGLNLQLAVI DVSGSKLSSS LLIGGKPAMV EEHMPLFLIN PTLSYTQSKE
110 120 130 140 150
ISNEGCLSFP GLRIDVPRSK RVKVKTFDLE GRPWYFEAGG FLSVAIQHEF
160 170 180 190
DHLQGKLFID YLSAEQKKAI KEELEKIKRG EAILSVKETD
Length:190
Mass (Da):21,388
Last modified:July 22, 2008 - v1
Checksum:i486AC49046D19A82
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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: November 26, 2014
This is version 41 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