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Protein

Peptide deformylase 2

Gene

def2

Organism
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Status
Reviewed-Annotation score: 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.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)DescriptionActionsGraphical viewLength
Metal bindingi110IronUniRule annotation1
Metal bindingi153IronUniRule annotation1
Active sitei154UniRule annotation1
Metal bindingi157IronUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BRENDAi3.5.1.88. 648.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 2UniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDF 2UniRule annotation
Alternative name(s):
Polypeptide deformylase 2UniRule annotation
Gene namesi
Name:def2UniRule annotation
Ordered Locus Names:BC_3974
OrganismiBacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Taxonomic identifieri226900 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillusBacillus cereus group
Proteomesi
  • UP000001417 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000827361 – 184Peptide deformylase 2Add BLAST184

Proteomic databases

PRIDEiQ819K2.

Interactioni

Protein-protein interaction databases

STRINGi226900.BC3974.

Structurei

Secondary structure

1184
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 6Combined sources3
Helixi13 – 16Combined sources4
Helixi28 – 44Combined sources17
Helixi47 – 52Combined sources6
Beta strandi59 – 62Combined sources4
Helixi63 – 66Combined sources4
Beta strandi70 – 78Combined sources9
Beta strandi84 – 97Combined sources14
Beta strandi99 – 103Combined sources5
Beta strandi123 – 133Combined sources11
Beta strandi138 – 144Combined sources7
Helixi145 – 158Combined sources14
Helixi163 – 166Combined sources4
Beta strandi177 – 181Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OKLX-ray1.70A/B1-184[»]
ProteinModelPortaliQ819K2.
SMRiQ819K2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ819K2.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
KOiK01462.
OMAiMILMKDI.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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.

Q819K2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLTMKDVIRE GDPILRNVAE EVSLPASEED TTTLKEMIEF VINSQDPEMA
60 70 80 90 100
EKYSLRPGIG LAAPQIGVSK KMIAVHVTDA DGTLYSHALF NPKIISHSVE
110 120 130 140 150
RTYLQGGEGC LSVDREVPGY VPRYTRITVK ATSINGEEVK LRLKGLPAIV
160 170 180
FQHEIDHLNG VMFYDHINKE NPFAAPDDSK PLER
Length:184
Mass (Da):20,474
Last modified:June 1, 2003 - v1
Checksum:i8B4E1CBE1CACA1F1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016877 Genomic DNA. Translation: AAP10894.1.
RefSeqiNP_833693.1. NC_004722.1.
WP_000957048.1. NC_004722.1.

Genome annotation databases

EnsemblBacteriaiAAP10894; AAP10894; BC_3974.
GeneIDi1206319.
KEGGibce:BC3974.
PATRICi32603994. VBIBacCer54481_4100.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016877 Genomic DNA. Translation: AAP10894.1.
RefSeqiNP_833693.1. NC_004722.1.
WP_000957048.1. NC_004722.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OKLX-ray1.70A/B1-184[»]
ProteinModelPortaliQ819K2.
SMRiQ819K2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi226900.BC3974.

Proteomic databases

PRIDEiQ819K2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAP10894; AAP10894; BC_3974.
GeneIDi1206319.
KEGGibce:BC3974.
PATRICi32603994. VBIBacCer54481_4100.

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.
KOiK01462.
OMAiMILMKDI.

Enzyme and pathway databases

BRENDAi3.5.1.88. 648.

Miscellaneous databases

EvolutionaryTraceiQ819K2.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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...

Entry informationi

Entry nameiDEF2_BACCR
AccessioniPrimary (citable) accession number: Q819K2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: June 1, 2003
Last modified: November 2, 2016
This is version 90 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, Reference proteome

Documents

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

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 one 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.