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Q68WP2 (PPDK_RICTY) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 63. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Pyruvate, phosphate dikinase

EC=2.7.9.1
Alternative name(s):
Pyruvate, orthophosphate dikinase
Gene names
Name:ppdK
Ordered Locus Names:RT0478
OrganismRickettsia typhi (strain ATCC VR-144 / Wilmington) [Complete proteome] [HAMAP]
Taxonomic identifier257363 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiatyphus group

Protein attributes

Sequence length880 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Catalyzes the reversible phosphorylation of pyruvate and phosphate By similarity.

Catalytic activity

ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate.

Cofactor

Magnesium By similarity.

Enzyme regulation

Activated by light-induced dephosphorylation. Inhibited by dark-induced phosphorylation. Both reactions are catalyzed by PDRP1 By similarity.

Subunit structure

Homodimer By similarity.

Domain

The N-terminal domain contains the ATP/Pi active site, the central domain the pyrophosphate/phosphate carrier histidine, and the C-terminal domain the pyruvate active site By similarity.

Post-translational modification

Phosphorylation of Thr-458 in the dark inactivates the enzyme. Dephosphorylation upon light stimulation reactivates the enzyme By similarity.

Miscellaneous

The reaction takes place in three steps, each mediated by a carrier histidine residue located on the surface of the central domain. The two first partial reactions are catalyzed at an active site located on the N-terminal domain, and the third partial reaction is catalyzed at an active site located on the C-terminal domain. For catalytic turnover, the central domain swivels from the concave surface of the N-terminal domain to that of the C-terminal domain.

Sequence similarities

Belongs to the PEP-utilizing enzyme family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 880880Pyruvate, phosphate dikinase
PRO_0000289279

Regions

Region1 – 348348N-terminal
Region349 – 40557Linker 1
Region406 – 50398Central
Region504 – 53835Linker 2
Region539 – 879341C-terminal

Sites

Active site4601Tele-phosphohistidine intermediate By similarity
Active site8361Proton donor By similarity
Metal binding7501Magnesium By similarity
Metal binding7741Magnesium By similarity
Binding site971ATP Potential
Binding site5661Substrate By similarity
Binding site6221Substrate By similarity
Binding site7501Substrate By similarity
Binding site7711Substrate; via carbonyl oxygen By similarity
Binding site7721Substrate; via amide nitrogen By similarity
Binding site7731Substrate By similarity
Binding site7741Substrate; via amide nitrogen By similarity

Amino acid modifications

Modified residue4581Phosphothreonine; by PDRP1 By similarity

Sequences

Sequence LengthMass (Da)Tools
Q68WP2 [UniParc].

Last modified October 11, 2004. Version 1.
Checksum: FFFE55AEEA138B34

FASTA88098,165
        10         20         30         40         50         60 
MNKLIYYFGN NGSDGNASMK NILGNKGAGL AEMSNLKLPI PNGFTITTEL CNYFYKHNNN 

        70         80         90        100        110        120 
LPKNFQNELQ QAITKLEITT GKIFGSTTSN PLLLSVRSGS TVSMPGMMDT ILNLGMNNEV 

       130        140        150        160        170        180 
CNALADSCGN KLFALDSYRR FLEMYGSTVL SIPSDLFEQI YEKHKVQADI YKDSDITVEL 

       190        200        210        220        230        240 
LEKIIDDFKR LHIKYTKQLI KDPYEQLESA IKAVLYSWKN NRAIVYRKLN NISEDFGTAI 

       250        260        270        280        290        300 
NIQEMVFGNL GKTSATGVVF TRSPSTGEKK LFGEFLINAQ GEDIVSGTRT PMPIIANDSN 

       310        320        330        340        350        360 
SMQAMMPEVF TKLSQIAKKL EEHYLDMQDI EFTIENNKLY ILQTRTAKRT AIAAINIAVQ 

       370        380        390        400        410        420 
MVEEKLISKE QALMRIDPES LNQLLHTRID YSKKLTAIAE GLPASPGAAT GIVVFSPYDA 

       430        440        450        460        470        480 
EKLSHHHKVI LVRHDTSPED INGMHVASGI LTIRGGMTSH AAVVARGMGK PCVCGTNNLS 

       490        500        510        520        530        540 
IDEQKQILIA GDIVIKQGDI ITIDGGSGKI FLGEMPLIQP TFSEESTLIL DWADEISSLK 

       550        560        570        580        590        600 
VRANAETVND ALVSIKFGAQ GIGLCRSEHM FFDKNKIPLV REMIIAPDIE RRQCALQKLL 

       610        620        630        640        650        660 
PLQTEDFKAL FRVMKNKPVN IRLLDPPLHE FLPTTDEDKK NLAHSLNLPL SMIHQRLHAM 

       670        680        690        700        710        720 
HEVNPMLGHR GCRLGICLPE IYQMQIEAIL TAIFELHKKE HIESNLELMI PLISNVAEIK 

       730        740        750        760        770        780 
KLKMDIYAVV KKLEQRYSYK FSFTLGTMIE LPRAALGSKK IAKEVDYFSF GTNDLTQTTY 

       790        800        810        820        830        840 
GISRDDIASF LPYYLEEKIF ESDPFTTLDE EGVGELIKIA IKRGKSSNAN LKLGACGEHA 

       850        860        870        880 
GNPTSIAFFH KMNLNYVSCS PYRIPIARIA AAQAKIKQGS 

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References

[1]"Complete genome sequence of Rickettsia typhi and comparison with sequences of other Rickettsiae."
McLeod M.P., Qin X., Karpathy S.E., Gioia J., Highlander S.K., Fox G.E., McNeill T.Z., Jiang H., Muzny D., Jacob L.S., Hawes A.C., Sodergren E., Gill R., Hume J., Morgan M., Fan G., Amin A.G., Gibbs R.A. expand/collapse author list , Hong C., Yu X.-J., Walker D.H., Weinstock G.M.
J. Bacteriol. 186:5842-5855(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC VR-144 / Wilmington.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE017197 Genomic DNA. Translation: AAU03950.1.
RefSeqYP_067432.1. NC_006142.1.

3D structure databases

ProteinModelPortalQ68WP2.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING257363.RT0478.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAU03950; AAU03950; RT0478.
GeneID2959286.
KEGGrty:RT0478.
PATRIC17910198. VBIRicTyp34752_0507.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0574.
HOGENOMHOG000039664.
KOK01006.
OMAAVFDSWN.
OrthoDBEOG6N0HGQ.
ProtClustDBPRK09279.

Enzyme and pathway databases

BioCycRTYP257363:GJEQ-501-MONOMER.

Family and domain databases

Gene3D3.20.20.60. 1 hit.
3.30.1490.20. 2 hits.
3.30.470.20. 1 hit.
3.50.30.10. 1 hit.
InterProIPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR008279. PEP-util_enz_mobile_dom.
IPR018274. PEP_util_AS.
IPR000121. PEP_util_C.
IPR023151. PEP_util_CS.
IPR002192. PPDK_PEP-bd.
IPR010121. Pyruvate_phosphate_dikinase.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PANTHERPTHR22931:SF9. PTHR22931:SF9. 1 hit.
PfamPF00391. PEP-utilizers. 1 hit.
PF02896. PEP-utilizers_C. 1 hit.
PF01326. PPDK_N. 1 hit.
[Graphical view]
PIRSFPIRSF000853. PPDK. 1 hit.
SUPFAMSSF51621. SSF51621. 1 hit.
SSF52009. SSF52009. 1 hit.
TIGRFAMsTIGR01828. pyru_phos_dikin. 1 hit.
PROSITEPS00742. PEP_ENZYMES_2. 1 hit.
PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePPDK_RICTY
AccessionPrimary (citable) accession number: Q68WP2
Entry history
Integrated into UniProtKB/Swiss-Prot: May 29, 2007
Last sequence update: October 11, 2004
Last modified: April 16, 2014
This is version 63 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Rickettsia typhi

Rickettsia typhi (strain Wilmington): entries and gene names