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Protein

Peptide deformylase 2

Gene
N/A
Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
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.

Catalytic activityi

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

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi110IronBy similarity1
Metal bindingi153IronBy similarity1
Active sitei154By similarity1
Metal bindingi157IronBy similarity1

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. 623.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 2 (EC:3.5.1.88)
Short name:
PDF 2
Alternative name(s):
Polypeptide deformylase 2
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000827381 – 184Peptide deformylase 2Add BLAST184

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 – 53Combined sources7
Beta strandi59 – 62Combined sources4
Helixi63 – 66Combined sources4
Beta strandi70 – 78Combined sources9
Beta strandi84 – 97Combined sources14
Beta strandi99 – 104Combined sources6
Beta strandi123 – 132Combined sources10
Beta strandi138 – 144Combined sources7
Helixi145 – 158Combined sources14
Helixi163 – 166Combined sources4
Beta strandi180 – 182Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LQYX-ray1.90A1-184[»]
ProteinModelPortaliO31410.
SMRiO31410.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO31410.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

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.

O31410-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MITMKDIIKE GHPTLRKVAE PVPLPPSEED KRILQSLLDY VKMSQDPELA
60 70 80 90 100
AKYGLRPGIG LAAPQINVSK RMIAVHVTDE NGTLYSYALF NPKIVSHSVQ
110 120 130 140 150
QCYLTTGEGC LSVDRDVPGY VLRYARITVT GTTLDGEEVT LRLKGLPAIV
160 170 180
FQHEIDHLNG IMFYDRINPA DPFQVPDGAI PIGR
Length:184
Mass (Da):20,383
Last modified:January 1, 1998 - v1
Checksum:i9CD85DEE53632FA0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y10549 Genomic DNA. Translation: CAA71581.1.
RefSeqiWP_033016217.1. NZ_LUCR01000041.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y10549 Genomic DNA. Translation: CAA71581.1.
RefSeqiWP_033016217.1. NZ_LUCR01000041.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LQYX-ray1.90A1-184[»]
ProteinModelPortaliO31410.
SMRiO31410.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.5.1.88. 623.

Miscellaneous databases

EvolutionaryTraceiO31410.

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_GEOSE
AccessioniPrimary (citable) accession number: O31410
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 92 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

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.