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Q45495

- DEF2_BACSU

UniProt

Q45495 - DEF2_BACSU

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Protein

Peptide deformylase 2

Gene

defB

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli

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.

Catalytic activityi

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

Cofactori

Fe2+By similarityNote: Binds 1 Fe(2+) ion.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi110 – 1101IronBy similarity
Metal bindingi153 – 1531IronBy similarity
Active sitei154 – 1541By similarity
Metal bindingi157 – 1571IronBy 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

BioCyciBSUB:BSU14560-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 2 (EC:3.5.1.88)
Short name:
PDF 2
Alternative name(s):
Polypeptide deformylase 2
Gene namesi
Name:defB
Synonyms:ykrB
Ordered Locus Names:BSU14560
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570: Chromosome

Organism-specific databases

GenoListiBSU14560. [Micado]

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 184184Peptide deformylase 2PRO_0000082740Add
BLAST

Proteomic databases

PaxDbiQ45495.

Interactioni

Protein-protein interaction databases

STRINGi224308.BSU14560.

Structurei

3D structure databases

ProteinModelPortaliQ45495.
SMRiQ45495. Positions 1-184.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243507.
InParanoidiQ45495.
KOiK01462.
OMAiHIDKENP.
OrthoDBiEOG6PZXGQ.
PhylomeDBiQ45495.

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.

Q45495-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MITMENIVRD GHPALRETAE PVELPPTDAE KQQLADMIEF VKNSQNPELA
60 70 80 90 100
EKYKLRPGVG LAAPQINIKK RMIAVHAEDA SGKLYSYALF NPKIVSHSVE
110 120 130 140 150
KSYLTSGEGC LSVDEAIPGY VPRYARIRVK GTTLEGENID IRLKGFPAIV
160 170 180
FQHEIDHLNG VMFYDHIDKE NPFKEPENAI AIER
Length:184
Mass (Da):20,656
Last modified:November 1, 1996 - v1
Checksum:i8641BF1932666C38
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF012285 Genomic DNA. Translation: AAC24930.1.
AL009126 Genomic DNA. Translation: CAB13329.1.
PIRiD69862.
RefSeqiNP_389339.1. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB13329; CAB13329; BSU14560.
GeneIDi939491.
KEGGibsu:BSU14560.
PATRICi18974703. VBIBacSub10457_1543.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF012285 Genomic DNA. Translation: AAC24930.1 .
AL009126 Genomic DNA. Translation: CAB13329.1 .
PIRi D69862.
RefSeqi NP_389339.1. NC_000964.3.

3D structure databases

ProteinModelPortali Q45495.
SMRi Q45495. Positions 1-184.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 224308.BSU14560.

Proteomic databases

PaxDbi Q45495.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CAB13329 ; CAB13329 ; BSU14560 .
GeneIDi 939491.
KEGGi bsu:BSU14560.
PATRICi 18974703. VBIBacSub10457_1543.

Organism-specific databases

GenoListi BSU14560. [Micado ]

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243507.
InParanoidi Q45495.
KOi K01462.
OMAi HIDKENP.
OrthoDBi EOG6PZXGQ.
PhylomeDBi Q45495.

Enzyme and pathway databases

BioCyci BSUB:BSU14560-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

« Hide 'large scale' publications
  1. "Sequence analysis of the mobA-ampS region of the Bacillus subtilis chromosome."
    Caldwell R.M., Ferrari E.
    Submitted (JUL-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "YkrB is the main peptide deformylase in Bacillus subtilis, a eubacterium containing two functional peptide deformylases."
    Haas M., Beyer D., Gahlmann R., Freiberg C.
    Microbiology 147:1783-1791(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.

Entry informationi

Entry nameiDEF2_BACSU
AccessioniPrimary (citable) accession number: Q45495
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1996
Last modified: November 26, 2014
This is version 107 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. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3