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Protein

Peptide deformylase

Gene

def

Organism
Synechococcus sp. (strain WH8102)
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 bindingi121 – 1211IronUniRule annotation
Metal bindingi163 – 1631IronUniRule annotation
Active sitei164 – 1641UniRule annotation
Metal bindingi167 – 1671IronUniRule 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 deformylaseUniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDFUniRule annotation
Alternative name(s):
Polypeptide deformylaseUniRule annotation
Gene namesi
Name:defUniRule annotation
Ordered Locus Names:SYNW0324
OrganismiSynechococcus sp. (strain WH8102)
Taxonomic identifieri84588 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus
ProteomesiUP000001422 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 201201Peptide deformylasePRO_0000082864Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi84588.SYNW0324.

Structurei

3D structure databases

ProteinModelPortaliQ7U9D4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiDTMLEMD.
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.

Q7U9D4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAGSFAQLAR AAEQSRDTML VPKTALETPP LEIHTLGAEV LRQSARRIGK
60 70 80 90 100
VTEQTRELAR DMLRSMYTAK GIGLAAPQVG IHQQLLVIDL DLENAATPPL
110 120 130 140 150
VLINPEISAA SASIDTYEEG CLSIPGVYLD VVRPTAIELS FRDEMGRPRK
160 170 180 190 200
MKADGLMARC IQHEMDHLNG VLFVDRVTDE AGLQKELKDH GFQRQHVQSV

S
Length:201
Mass (Da):22,123
Last modified:October 1, 2003 - v1
Checksum:i96ED79F01249FA48
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX569689 Genomic DNA. Translation: CAE06839.1.
RefSeqiNP_896419.1. NC_005070.1.
WP_011127198.1. NC_005070.1.

Genome annotation databases

KEGGisyw:SYNW0324.
PATRICi23832037. VBISynSp27240_0329.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX569689 Genomic DNA. Translation: CAE06839.1.
RefSeqiNP_896419.1. NC_005070.1.
WP_011127198.1. NC_005070.1.

3D structure databases

ProteinModelPortaliQ7U9D4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi84588.SYNW0324.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGisyw:SYNW0324.
PATRICi23832037. VBISynSp27240_0329.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiDTMLEMD.
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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: WH8102.

Entry informationi

Entry nameiDEF_SYNPX
AccessioniPrimary (citable) accession number: Q7U9D4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: October 1, 2003
Last modified: April 1, 2015
This is version 67 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.