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Q8DP79

- DEF_STRR6

UniProt

Q8DP79 - DEF_STRR6

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Protein

Peptide deformylase

Gene

def

Organism
Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
Status
Reviewed - Annotation score: 2 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 Fe(2+) ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi130 – 1301IronUniRule annotation
Metal bindingi173 – 1731IronUniRule annotation
Active sitei174 – 1741UniRule annotation
Metal bindingi177 – 1771IronUniRule 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

Enzyme and pathway databases

BioCyciSPNE171101:GJC8-1323-MONOMER.

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:spr1310
OrganismiStreptococcus pneumoniae (strain ATCC BAA-255 / R6)
Taxonomic identifieri171101 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
ProteomesiUP000000586: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 203203Peptide deformylasePRO_0000082858Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi171101.spr1310.

Structurei

Secondary structure

1
203
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 75Combined sources
Helixi16 – 183Combined sources
Helixi25 – 284Combined sources
Helixi40 – 5617Combined sources
Helixi59 – 657Combined sources
Beta strandi71 – 744Combined sources
Helixi75 – 784Combined sources
Beta strandi82 – 909Combined sources
Beta strandi103 – 11715Combined sources
Beta strandi119 – 1246Combined sources
Beta strandi143 – 1453Combined sources
Beta strandi147 – 1526Combined sources
Beta strandi158 – 1636Combined sources
Helixi165 – 17814Combined sources
Helixi183 – 1864Combined sources
Beta strandi189 – 1913Combined sources
Beta strandi199 – 2024Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AI7X-ray2.00A1-202[»]
2AIAX-ray1.70A1-202[»]
2AIEX-ray1.70P1-202[»]
4EOXX-ray1.78P1-203[»]
ProteinModelPortaliQ8DP79.
SMRiQ8DP79. Positions 2-203.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8DP79.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243507.
KOiK01462.
OMAiIISCKIL.
OrthoDBiEOG6PZXGQ.

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.

Q8DP79-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSAIERITKA AHLIDMNDII REGNPTLRTV AEEVTFPLSD QEIILGEKMM
60 70 80 90 100
QFLKHSQDPV MAEKMGLRGG VGLAAPQLDI SKRIIAVLVP NIVEEGETPQ
110 120 130 140 150
EAYDLEAIMY NPKIVSHSVQ DAALGEGEGC LSVDRNVPGY VVRHARVTVD
160 170 180 190 200
YFDKDGEKHR IKLKGYNSIV VQHEIDHING IMFYDRINEK DPFAVKDGLL

ILE
Length:203
Mass (Da):22,692
Last modified:March 1, 2003 - v1
Checksum:iE332956982A67161
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007317 Genomic DNA. Translation: AAL00114.1.
PIRiE98035.
RefSeqiNP_358903.1. NC_003098.1.

Genome annotation databases

EnsemblBacteriaiAAL00114; AAL00114; spr1310.
GeneIDi934523.
KEGGispr:spr1310.
PATRICi19702614. VBIStrPne107296_1422.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007317 Genomic DNA. Translation: AAL00114.1 .
PIRi E98035.
RefSeqi NP_358903.1. NC_003098.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2AI7 X-ray 2.00 A 1-202 [» ]
2AIA X-ray 1.70 A 1-202 [» ]
2AIE X-ray 1.70 P 1-202 [» ]
4EOX X-ray 1.78 P 1-203 [» ]
ProteinModelPortali Q8DP79.
SMRi Q8DP79. Positions 2-203.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 171101.spr1310.

Chemistry

BindingDBi Q8DP79.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL00114 ; AAL00114 ; spr1310 .
GeneIDi 934523.
KEGGi spr:spr1310.
PATRICi 19702614. VBIStrPne107296_1422.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243507.
KOi K01462.
OMAi IISCKIL.
OrthoDBi EOG6PZXGQ.

Enzyme and pathway databases

BioCyci SPNE171101:GJC8-1323-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q8DP79.

Family and domain databases

Gene3Di 3.90.45.10. 1 hit.
HAMAPi MF_00163. Pep_deformylase.
InterProi IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view ]
PANTHERi PTHR10458. PTHR10458. 1 hit.
Pfami PF01327. Pep_deformylase. 1 hit.
[Graphical view ]
PIRSFi PIRSF004749. Pep_def. 1 hit.
PRINTSi PR01576. PDEFORMYLASE.
SUPFAMi SSF56420. SSF56420. 1 hit.
TIGRFAMsi TIGR00079. pept_deformyl. 1 hit.
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-255 / R6.

Entry informationi

Entry nameiDEF_STRR6
AccessioniPrimary (citable) accession number: Q8DP79
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: March 1, 2003
Last modified: November 26, 2014
This is version 84 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

External Data

Dasty 3