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A5VDM3

- DEF_SPHWW

UniProt

A5VDM3 - DEF_SPHWW

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Protein
Peptide deformylase
Gene
def, Swit_4045
Organism
Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
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 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 bindingi99 – 991Iron By similarity
Metal bindingi141 – 1411Iron By similarity
Active sitei142 – 1421 By similarity
Metal bindingi145 – 1451Iron 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

BioCyciSWIT392499:GHZK-4094-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
Ordered Locus Names:Swit_4045
OrganismiSphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
Taxonomic identifieri392499 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingomonas
ProteomesiUP000001989: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 177177Peptide deformylaseUniRule annotation
PRO_1000023135Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi392499.Swit_4045.

Structurei

3D structure databases

ProteinModelPortaliA5VDM3.
SMRiA5VDM3. Positions 2-174.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEETGEEW.
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.

A5VDM3-1 [UniParc]FASTAAdd to Basket

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MAIRLILEAP DPRLRTISTP VEAVDDELRA LIADMFETMY DAPGIGLAAI    50
QVGVPKRVLV IDLQEEEDAE GKPIRHPRVF INPELFDPSE EQSVYNEGCL 100
SVPEQYAEVE RPAVIHARWL DEQGAKHEER LEGLLATCLQ HEMDHLEGIL 150
FIDHLSRLKR EMVMKKLEKA RRARKAA 177
Length:177
Mass (Da):20,154
Last modified:July 10, 2007 - v1
Checksum:i1A62E4EA8CF88867
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000699 Genomic DNA. Translation: ABQ70389.1.
RefSeqiWP_012050228.1. NC_009511.1.
YP_001264527.1. NC_009511.1.

Genome annotation databases

EnsemblBacteriaiABQ70389; ABQ70389; Swit_4045.
GeneIDi5198978.
KEGGiswi:Swit_4045.
PATRICi23687377. VBISphWit55028_4617.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000699 Genomic DNA. Translation: ABQ70389.1 .
RefSeqi WP_012050228.1. NC_009511.1.
YP_001264527.1. NC_009511.1.

3D structure databases

ProteinModelPortali A5VDM3.
SMRi A5VDM3. Positions 2-174.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 392499.Swit_4045.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABQ70389 ; ABQ70389 ; Swit_4045 .
GeneIDi 5198978.
KEGGi swi:Swit_4045.
PATRICi 23687377. VBISphWit55028_4617.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243509.
KOi K01462.
OMAi EETGEEW.
OrthoDBi EOG664CMF.

Enzyme and pathway databases

BioCyci SWIT392499:GHZK-4094-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: RW1 / DSM 6014 / JCM 10273.

Entry informationi

Entry nameiDEF_SPHWW
AccessioniPrimary (citable) accession number: A5VDM3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 10, 2007
Last modified: September 3, 2014
This is version 48 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi