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Q5HGZ3

- DEF_STAAC

UniProt

Q5HGZ3 - DEF_STAAC

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Protein
Peptide deformylase
Gene
def, def1, pdf1, SACOL1100
Organism
Staphylococcus aureus (strain COL)
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 By similarity.UniRule annotation

Catalytic activityi

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

Cofactori

Binds 1 Fe2+ ion By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi111 – 1111Iron By similarity
Metal bindingi154 – 1541Iron By similarity
Active sitei155 – 1551 By similarity
Metal bindingi158 – 1581Iron By 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

BioCyciSAUR93062:GCEP-1085-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase (EC:3.5.1.88)
Short name:
PDF
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:def
Synonyms:def1, pdf1
Ordered Locus Names:SACOL1100
OrganismiStaphylococcus aureus (strain COL)
Taxonomic identifieri93062 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcus
ProteomesiUP000000530: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 183183Peptide deformylaseUniRule annotation
PRO_0000082838Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi93062.SACOL1100.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 63
Helixi13 – 164
Helixi28 – 4417
Helixi47 – 526
Beta strandi59 – 624
Helixi63 – 664
Beta strandi70 – 778
Beta strandi81 – 833
Beta strandi86 – 9813
Beta strandi100 – 1045
Beta strandi124 – 13310
Beta strandi139 – 1468
Helixi147 – 15913
Helixi164 – 1674
Beta strandi170 – 1723

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3U7KX-ray1.90A1-183[»]
3U7LX-ray2.01A1-183[»]
3U7MX-ray2.15A1-183[»]
3U7NX-ray2.30A1-183[»]
ProteinModelPortaliQ5HGZ3.
SMRiQ5HGZ3. Positions 1-183.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243507.
KOiK01462.
OMAiHIDKENP.
OrthoDBiEOG6PZXGQ.

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.

Q5HGZ3-1 [UniParc]FASTAAdd to Basket

« Hide

MLTMKDIIRD GHPTLRQKAA ELELPLTKEE KETLIAMREF LVNSQDEEIA    50
KRYGLRSGVG LAAPQINISK RMIAVLIPDD GSGKSYDYML VNPKIVSHSV 100
QEAYLPTGEG CLSVDDNVAG LVHRHNRITI KAKDIEGNDI QLRLKGYPAI 150
VFQHEIDHLN GVMFYDHIDK DHPLQPHTDA VEV 183
Length:183
Mass (Da):20,560
Last modified:February 15, 2005 - v1
Checksum:i32A64066AE5CAB0E
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000046 Genomic DNA. Translation: AAW37980.1.
RefSeqiYP_185964.1. NC_002951.2.

Genome annotation databases

EnsemblBacteriaiAAW37980; AAW37980; SACOL1100.
GeneIDi3237843.
KEGGisac:SACOL1100.
PATRICi19528440. VBIStaAur112458_1073.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000046 Genomic DNA. Translation: AAW37980.1 .
RefSeqi YP_185964.1. NC_002951.2.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3U7K X-ray 1.90 A 1-183 [» ]
3U7L X-ray 2.01 A 1-183 [» ]
3U7M X-ray 2.15 A 1-183 [» ]
3U7N X-ray 2.30 A 1-183 [» ]
ProteinModelPortali Q5HGZ3.
SMRi Q5HGZ3. Positions 1-183.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 93062.SACOL1100.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAW37980 ; AAW37980 ; SACOL1100 .
GeneIDi 3237843.
KEGGi sac:SACOL1100.
PATRICi 19528440. VBIStaAur112458_1073.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243507.
KOi K01462.
OMAi HIDKENP.
OrthoDBi EOG6PZXGQ.

Enzyme and pathway databases

BioCyci SAUR93062:GCEP-1085-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. "Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain."
    Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J., Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J., Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H., Vamathevan J.J., Khouri H.
    , Utterback T.R., Lee C., Dimitrov G., Jiang L., Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E., Fraser C.M.
    J. Bacteriol. 187:2426-2438(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: COL.

Entry informationi

Entry nameiDEF_STAAC
AccessioniPrimary (citable) accession number: Q5HGZ3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: February 15, 2005
Last modified: May 14, 2014
This is version 60 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

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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