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Protein

Peptide deformylase 1

Gene

def1

Organism
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Status
Reviewed-Annotation score: 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.UniRule annotation

Catalytic activityi

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

Cofactori

Fe2+UniRule annotationNote: Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi93 – 931IronUniRule annotation
Metal bindingi135 – 1351IronUniRule annotation
Active sitei136 – 1361UniRule annotation
Metal bindingi139 – 1391IronUniRule 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

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:Cgl1601, cg1804
OrganismiCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Taxonomic identifieri196627 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeCorynebacteriaceaeCorynebacterium
ProteomesiUP000000582: Chromosome, UP000001009: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 169169Peptide deformylase 1PRO_0000082774Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi196627.cg1804.

Structurei

3D structure databases

ProteinModelPortaliQ8NQ46.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiRHGKDNN.
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.

Q8NQ46-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAVREVRLFG DPVLVSRADE VVDFDESLST LIDDMFDTME DAGGVGLAAN
60 70 80 90 100
QVGVLRRVFV FDTSHQEGGL RGHVINPVWE PLTEDTQTGK EGCLSIPDVS
110 120 130 140 150
AETTRYETVR LSGQDRDGNP VGFVANGLLA RCIQHETDHL DGVLFLKRLD
160
PAERKAAMGV IRASAWFNK
Length:169
Mass (Da):18,543
Last modified:October 1, 2002 - v1
Checksum:iCD962574BFB74329
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000036 Genomic DNA. Translation: BAB98994.1.
BX927152 Genomic DNA. Translation: CAF21609.1.
RefSeqiNP_600815.1. NC_003450.3.
YP_225885.1. NC_006958.1.

Genome annotation databases

EnsemblBacteriaiBAB98994; BAB98994; BAB98994.
CAF21609; CAF21609; cg1804.
GeneIDi1019569.
3343555.
KEGGicgb:cg1804.
cgl:NCgl1539.
PATRICi21495239. VBICorGlu203724_1563.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000036 Genomic DNA. Translation: BAB98994.1.
BX927152 Genomic DNA. Translation: CAF21609.1.
RefSeqiNP_600815.1. NC_003450.3.
YP_225885.1. NC_006958.1.

3D structure databases

ProteinModelPortaliQ8NQ46.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi196627.cg1804.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB98994; BAB98994; BAB98994.
CAF21609; CAF21609; cg1804.
GeneIDi1019569.
3343555.
KEGGicgb:cg1804.
cgl:NCgl1539.
PATRICi21495239. VBICorGlu203724_1563.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiRHGKDNN.
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.
ProtoNetiSearch...

Publicationsi

  1. "The Corynebacterium glutamicum genome: features and impacts on biotechnological processes."
    Ikeda M., Nakagawa S.
    Appl. Microbiol. Biotechnol. 62:99-109(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.

Entry informationi

Entry nameiDEF1_CORGL
AccessioniPrimary (citable) accession number: Q8NQ46
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: October 1, 2002
Last modified: February 4, 2015
This is version 75 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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.