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A5VDM3 (DEF_SPHWW) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 43. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Peptide deformylase
Short name=PDF
EC=3.5.1.88
Alternative name(s):
Polypeptide deformylase
Gene names
Name:def
Ordered Locus Names:Swit_4045
OrganismSphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273) [Complete proteome] [HAMAP]
Taxonomic identifier392499 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Sphingomonadales › Sphingomonadaceae › Sphingomonas ›

Protein attributes

Sequence length177 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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. HAMAP-Rule MF_00163

Catalytic activity

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP-Rule MF_00163

Cofactor

Binds 1 Fe2+ ion By similarity. HAMAP-Rule MF_00163

Sequence similarities

Belongs to the polypeptide deformylase family.

Ontologies

Keywords
   Biological processProtein biosynthesis
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological_processtranslation

Inferred from electronic annotation. Source: HAMAP

   Molecular_functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 177177Peptide deformylase HAMAP-Rule MF_00163
PRO_1000023135

Sites

Active site1421 By similarity
Metal binding991Iron By similarity
Metal binding1411Iron By similarity
Metal binding1451Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
A5VDM3 [UniParc].

Last modified July 10, 2007. Version 1.
Checksum: 1A62E4EA8CF88867

FASTA17720,154
        10         20         30         40         50         60 
MAIRLILEAP DPRLRTISTP VEAVDDELRA LIADMFETMY DAPGIGLAAI QVGVPKRVLV 

        70         80         90        100        110        120 
IDLQEEEDAE GKPIRHPRVF INPELFDPSE EQSVYNEGCL SVPEQYAEVE RPAVIHARWL 

       130        140        150        160        170 
DEQGAKHEER LEGLLATCLQ HEMDHLEGIL FIDHLSRLKR EMVMKKLEKA RRARKAA

« Hide

References

[1]"Complete sequence of chromosome of Sphingomonas wittichii RW1."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Saunders E., Brettin T., Bruce D., Detter J.C., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M. expand/collapse author list , Hauser L., Kyrpides N., Kim E., Halden R.U., Miller T.R., Salzberg S.L., Eisen J.A., Richardson P.
Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: RW1 / DSM 6014 / JCM 10273.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000699 Genomic DNA. Translation: ABQ70389.1.
RefSeqYP_001264527.1. NC_009511.1.

3D structure databases

ProteinModelPortalA5VDM3.
SMRA5VDM3. Positions 2-174.
ModBaseSearch...

Protein-protein interaction databases

STRING392499.Swit_4045.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABQ70389; ABQ70389; Swit_4045.
GeneID5198978.
KEGGswi:Swit_4045.
PATRIC23687377. VBISphWit55028_4617.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAVHERIIT.
ProtClustDBCLSK2791006.

Enzyme and pathway databases

BioCycSWIT392499:GHZK-4094-MONOMER.

Family and domain databases

Gene3D3.90.45.10. 1 hit.
HAMAPMF_00163. Pep_deformylase.
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERPTHR10458. PTHR10458. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFPIRSF004749. Pep_def. 1 hit.
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. Fmet_deformylase. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF_SPHWW
AccessionPrimary (citable) accession number: A5VDM3
Entry history
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 10, 2007
Last modified: May 29, 2013
This is version 43 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

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