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Protein

Peptide deformylase

Gene

def

Organism
Staphylococcus aureus
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 (By similarity).By similarity

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 bindingi111Iron1
Metal bindingi154Iron1
Active sitei155By similarity1
Metal bindingi158Iron1

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. 3352.

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
Synonyms:def1, pdf1
OrganismiStaphylococcus aureus
Taxonomic identifieri1280 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL2010635.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000828431 – 183Peptide deformylaseAdd BLAST183

Proteomic databases

PRIDEiP68826.

Interactioni

Protein-protein interaction databases

STRINGi93062.SACOL1100.

Chemistry databases

BindingDBiP68826.

Structurei

Secondary structure

1183
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 6Combined sources3
Helixi13 – 16Combined sources4
Helixi28 – 45Combined sources18
Helixi47 – 53Combined sources7
Beta strandi58 – 62Combined sources5
Helixi63 – 66Combined sources4
Beta strandi70 – 77Combined sources8
Beta strandi81 – 83Combined sources3
Beta strandi86 – 98Combined sources13
Beta strandi100 – 104Combined sources5
Beta strandi124 – 133Combined sources10
Beta strandi139 – 145Combined sources7
Helixi146 – 159Combined sources14
Helixi164 – 167Combined sources4
Beta strandi170 – 172Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LM4X-ray1.45A/B1-183[»]
1LMHX-ray1.90A1-183[»]
1LQWX-ray1.87A/B1-183[»]
1Q1YX-ray1.90A1-183[»]
2AI9X-ray2.50A/B1-183[»]
ProteinModelPortaliP68826.
SMRiP68826.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP68826.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.

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.

P68826-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLTMKDIIRD GHPTLRQKAA ELELPLTKEE KETLIAMREF LVNSQDEEIA
60 70 80 90 100
KRYGLRSGVG LAAPQINISK RMIAVLIPDD GSGKSYDYML VNPKIVSHSV
110 120 130 140 150
QEAYLPTGEG CLSVDDNVAG LVHRHNRITI KAKDIEGNDI QLRLKGYPAI
160 170 180
VFQHEIDHLN GVMFYDHIDK NHPLQPHTDA VEV
Length:183
Mass (Da):20,559
Last modified:December 21, 2004 - v1
Checksum:i32A64066A6FEAB0E
GO

Mass spectrometryi

Molecular mass is 20600 Da from positions 1 - 183. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY007227 Genomic DNA. Translation: AAG02249.1.
RefSeqiWP_000957037.1. NZ_MAQQ01000003.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY007227 Genomic DNA. Translation: AAG02249.1.
RefSeqiWP_000957037.1. NZ_MAQQ01000003.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LM4X-ray1.45A/B1-183[»]
1LMHX-ray1.90A1-183[»]
1LQWX-ray1.87A/B1-183[»]
1Q1YX-ray1.90A1-183[»]
2AI9X-ray2.50A/B1-183[»]
ProteinModelPortaliP68826.
SMRiP68826.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi93062.SACOL1100.

Chemistry databases

BindingDBiP68826.
ChEMBLiCHEMBL2010635.

Proteomic databases

PRIDEiP68826.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4108Z02. Bacteria.
COG0242. LUCA.

Enzyme and pathway databases

BRENDAi3.5.1.88. 3352.

Miscellaneous databases

EvolutionaryTraceiP68826.

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 nameiDEF_STAAU
AccessioniPrimary (citable) accession number: P68826
Secondary accession number(s): Q9F4L4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 21, 2004
Last sequence update: December 21, 2004
Last modified: November 30, 2016
This is version 68 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.