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B2RMJ1

- DEF_PORG3

UniProt

B2RMJ1 - DEF_PORG3

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Protein

Peptide deformylase

Gene

def

Organism
Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257)
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 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

BioCyciPGIN431947:GC9J-2128-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:PGN_2068
OrganismiPorphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257)
Taxonomic identifieri431947 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesPorphyromonadaceaePorphyromonas
ProteomesiUP000008842: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 189189Peptide deformylasePRO_1000097333Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi431947.PGN_2068.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEETGEEW.
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.

B2RMJ1-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MLLPIYLYGH PVLRKVAEDI TPDYPKLKEL IANMTESMYH SDGIGLAAPQ
60 70 80 90 100
IGLPIRVLVI DADPLKEDYP ECAGFKRVMI NAHIEERGED LCTEYEGCLS
110 120 130 140 150
LPAIHEKVER PTSIRIRYVD EDFQPHEEVL HGFAARVVQH EYDHIDGKLF
160 170 180
IDHISPIRKQ LIKGKLQNII KGKVRTSYRV VTAPTGKRR
Length:189
Mass (Da):21,592
Last modified:July 1, 2008 - v1
Checksum:i8D0169D50273145E
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP009380 Genomic DNA. Translation: BAG34586.1.
RefSeqiWP_012458729.1. NC_010729.1.
YP_001930183.1. NC_010729.1.

Genome annotation databases

EnsemblBacteriaiBAG34586; BAG34586; PGN_2068.
GeneIDi6330572.
KEGGipgn:PGN_2068.
PATRICi22977099. VBIPorGin26334_2032.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP009380 Genomic DNA. Translation: BAG34586.1 .
RefSeqi WP_012458729.1. NC_010729.1.
YP_001930183.1. NC_010729.1.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 431947.PGN_2068.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAG34586 ; BAG34586 ; PGN_2068 .
GeneIDi 6330572.
KEGGi pgn:PGN_2068.
PATRICi 22977099. VBIPorGin26334_2032.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyci PGIN431947:GC9J-2128-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. "Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis."
    Naito M., Hirakawa H., Yamashita A., Ohara N., Shoji M., Yukitake H., Nakayama K., Toh H., Yoshimura F., Kuhara S., Hattori M., Hayashi T., Nakayama K.
    DNA Res. 15:215-225(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 33277 / DSM 20709 / JCM 12257.

Entry informationi

Entry nameiDEF_PORG3
AccessioniPrimary (citable) accession number: B2RMJ1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 1, 2008
Last modified: October 1, 2014
This is version 44 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