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Q89BN9

- DEF_BRADU

UniProt

Q89BN9 - DEF_BRADU

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Protein

Peptide deformylase

Gene

def

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
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

BioCyciBJAP224911:GJEJ-8167-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:bll8109
OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Taxonomic identifieri224911 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
ProteomesiUP000002526: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 174174Peptide deformylasePRO_0000082751Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi224911.bll8109.

Structurei

3D structure databases

ProteinModelPortaliQ89BN9.
SMRiQ89BN9. Positions 2-172.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
InParanoidiQ89BN9.
KOiK01462.
OrthoDBiEOG664CMF.
PhylomeDBiQ89BN9.

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.

Q89BN9-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MALREIIILP DKQLRLVSKP IEKVTTEIRK LADDMFETMY DAPGIGLAAI
60 70 80 90 100
QIAQPLRLIT MDLAKRDENG ETKPEPRVFI NPEVIASSEE LSVYEEGCLS
110 120 130 140 150
IPEYYEEVER PAKVRVRFTD LDGKVHEEDA EGLYATCIQH EIDHLNGVLF
160 170
VDYLSKLKRD RVLKKFEKAA KRAE
Length:174
Mass (Da):19,930
Last modified:June 1, 2003 - v1
Checksum:iC4D96157F6D26558
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000040 Genomic DNA. Translation: BAC53374.1.
RefSeqiNP_774749.1. NC_004463.1.

Genome annotation databases

EnsemblBacteriaiBAC53374; BAC53374; BAC53374.
GeneIDi1049081.
KEGGibja:bll8109.
PATRICi21200236. VBIBraJap65052_8344.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000040 Genomic DNA. Translation: BAC53374.1 .
RefSeqi NP_774749.1. NC_004463.1.

3D structure databases

ProteinModelPortali Q89BN9.
SMRi Q89BN9. Positions 2-172.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 224911.bll8109.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAC53374 ; BAC53374 ; BAC53374 .
GeneIDi 1049081.
KEGGi bja:bll8109.
PATRICi 21200236. VBIBraJap65052_8344.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243509.
InParanoidi Q89BN9.
KOi K01462.
OrthoDBi EOG664CMF.
PhylomeDBi Q89BN9.

Enzyme and pathway databases

BioCyci BJAP224911:GJEJ-8167-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110.

Entry informationi

Entry nameiDEF_BRADU
AccessioniPrimary (citable) accession number: Q89BN9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: June 1, 2003
Last modified: October 29, 2014
This is version 67 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