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Q8PGV2

- DEF1_XANAC

UniProt

Q8PGV2 - DEF1_XANAC

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Protein

Peptide deformylase 1

Gene

def1

Organism
Xanthomonas axonopodis pv. citri (strain 306)
Status
Reviewed - Annotation score: 3 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 bindingi99 – 991IronUniRule annotation
Metal bindingi141 – 1411IronUniRule annotation
Active sitei142 – 1421UniRule 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

BioCyciXAXO190486:GH55-3510-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1UniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDF 1UniRule annotation
Alternative name(s):
Polypeptide deformylase 1UniRule annotation
Gene namesi
Name:def1UniRule annotation
Ordered Locus Names:XAC3510
OrganismiXanthomonas axonopodis pv. citri (strain 306)
Taxonomic identifieri190486 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
ProteomesiUP000000576: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 171171Peptide deformylase 1PRO_0000082883Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi190486.XAC3510.

Structurei

3D structure databases

ProteinModelPortaliQ8PGV2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiETMHDAN.
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.

Q8PGV2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MIREIIRMGD KRLLRVAPPV TNLGSAELHT LVADMFETMD AARGVGLAAP
60 70 80 90 100
QIAVDLQLMV FGFDASERYP EAPAVPRTAL ANAQIEPLSE DMENGWEGCL
110 120 130 140 150
SIPGLRAVIP RYRFIRYRGF APDGSPIERD AEGFHARVVQ HEYDNLVGRL
160 170
YPSRIENFDT FGFEDVLSYD L
Length:171
Mass (Da):19,142
Last modified:October 1, 2002 - v1
Checksum:i983EDE2F995723F1
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE008923 Genomic DNA. Translation: AAM38353.1.
RefSeqiNP_643817.1. NC_003919.1.
WP_011052322.1. NC_003919.1.

Genome annotation databases

EnsemblBacteriaiAAM38353; AAM38353; XAC3510.
GeneIDi1157581.
KEGGixac:XAC3510.
PATRICi24059162. VBIXanAxo33670_3632.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE008923 Genomic DNA. Translation: AAM38353.1 .
RefSeqi NP_643817.1. NC_003919.1.
WP_011052322.1. NC_003919.1.

3D structure databases

ProteinModelPortali Q8PGV2.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 190486.XAC3510.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAM38353 ; AAM38353 ; XAC3510 .
GeneIDi 1157581.
KEGGi xac:XAC3510.
PATRICi 24059162. VBIXanAxo33670_3632.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243508.
KOi K01462.
OMAi ETMHDAN.
OrthoDBi EOG664CMF.

Enzyme and pathway databases

BioCyci XAXO190486:GH55-3510-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. "Comparison of the genomes of two Xanthomonas pathogens with differing host specificities."
    da Silva A.C.R., Ferro J.A., Reinach F.C., Farah C.S., Furlan L.R., Quaggio R.B., Monteiro-Vitorello C.B., Van Sluys M.A., Almeida N.F. Jr., Alves L.M.C., do Amaral A.M., Bertolini M.C., Camargo L.E.A., Camarotte G., Cannavan F., Cardozo J., Chambergo F., Ciapina L.P.
    , Cicarelli R.M.B., Coutinho L.L., Cursino-Santos J.R., El-Dorry H., Faria J.B., Ferreira A.J.S., Ferreira R.C.C., Ferro M.I.T., Formighieri E.F., Franco M.C., Greggio C.C., Gruber A., Katsuyama A.M., Kishi L.T., Leite R.P., Lemos E.G.M., Lemos M.V.F., Locali E.C., Machado M.A., Madeira A.M.B.N., Martinez-Rossi N.M., Martins E.C., Meidanis J., Menck C.F.M., Miyaki C.Y., Moon D.H., Moreira L.M., Novo M.T.M., Okura V.K., Oliveira M.C., Oliveira V.R., Pereira H.A., Rossi A., Sena J.A.D., Silva C., de Souza R.F., Spinola L.A.F., Takita M.A., Tamura R.E., Teixeira E.C., Tezza R.I.D., Trindade dos Santos M., Truffi D., Tsai S.M., White F.F., Setubal J.C., Kitajima J.P.
    Nature 417:459-463(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 306.

Entry informationi

Entry nameiDEF1_XANAC
AccessioniPrimary (citable) accession number: Q8PGV2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: October 1, 2002
Last modified: October 29, 2014
This is version 77 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

The third iron-binding site which is normally a His is replaced here by Asn-145.Curated

Keywords - Technical termi

Complete proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3