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Protein

Pyruvate, phosphate dikinase

Gene

ppdK

Organism
Rickettsia typhi (strain ATCC VR-144 / Wilmington)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the reversible phosphorylation of pyruvate and phosphate.By similarity

Catalytic activityi

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

Cofactori

Mg2+By similarity

Enzyme regulationi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei97 – 971ATPSequence Analysis
Active sitei460 – 4601Tele-phosphohistidine intermediateBy similarity
Binding sitei566 – 5661SubstrateBy similarity
Binding sitei622 – 6221SubstrateBy similarity
Metal bindingi750 – 7501MagnesiumBy similarity
Binding sitei750 – 7501SubstrateBy similarity
Binding sitei771 – 7711Substrate; via carbonyl oxygenBy similarity
Binding sitei772 – 7721Substrate; via amide nitrogenBy similarity
Binding sitei773 – 7731SubstrateBy similarity
Metal bindingi774 – 7741MagnesiumBy similarity
Binding sitei774 – 7741Substrate; via amide nitrogenBy similarity
Active sitei836 – 8361Proton donorBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. kinase activity Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW
  4. pyruvate, phosphate dikinase activity Source: UniProtKB-EC

GO - Biological processi

  1. pyruvate metabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciRTYP257363:GJEQ-501-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvate, phosphate dikinase (EC:2.7.9.1)
Alternative name(s):
Pyruvate, orthophosphate dikinase
Gene namesi
Name:ppdK
Ordered Locus Names:RT0478
OrganismiRickettsia typhi (strain ATCC VR-144 / Wilmington)
Taxonomic identifieri257363 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiatyphus group
ProteomesiUP000000604 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 880880Pyruvate, phosphate dikinasePRO_0000289279Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei458 – 4581Phosphothreonine; by PDRP1By similarity

Post-translational modificationi

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

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi257363.RT0478.

Structurei

3D structure databases

ProteinModelPortaliQ68WP2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 348348N-terminalAdd
BLAST
Regioni349 – 40557Linker 1Add
BLAST
Regioni406 – 50398CentralAdd
BLAST
Regioni504 – 53835Linker 2Add
BLAST
Regioni539 – 879341C-terminalAdd
BLAST

Domaini

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

Sequence similaritiesi

Belongs to the PEP-utilizing enzyme family.Curated

Phylogenomic databases

eggNOGiCOG0574.
HOGENOMiHOG000039664.
KOiK01006.
OMAiVRRETNP.
OrthoDBiEOG6N0HGQ.

Family and domain databases

Gene3Di3.20.20.60. 1 hit.
3.30.1490.20. 2 hits.
3.30.470.20. 1 hit.
3.50.30.10. 1 hit.
InterProiIPR013815. 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]
PANTHERiPTHR22931:SF9. PTHR22931:SF9. 1 hit.
PfamiPF00391. PEP-utilizers. 1 hit.
PF02896. PEP-utilizers_C. 1 hit.
PF01326. PPDK_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000853. PPDK. 1 hit.
SUPFAMiSSF51621. SSF51621. 1 hit.
SSF52009. SSF52009. 1 hit.
TIGRFAMsiTIGR01828. pyru_phos_dikin. 1 hit.
PROSITEiPS00742. PEP_ENZYMES_2. 1 hit.
PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q68WP2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNKLIYYFGN NGSDGNASMK NILGNKGAGL AEMSNLKLPI PNGFTITTEL
60 70 80 90 100
CNYFYKHNNN LPKNFQNELQ QAITKLEITT GKIFGSTTSN PLLLSVRSGS
110 120 130 140 150
TVSMPGMMDT ILNLGMNNEV CNALADSCGN KLFALDSYRR FLEMYGSTVL
160 170 180 190 200
SIPSDLFEQI YEKHKVQADI YKDSDITVEL LEKIIDDFKR LHIKYTKQLI
210 220 230 240 250
KDPYEQLESA IKAVLYSWKN NRAIVYRKLN NISEDFGTAI NIQEMVFGNL
260 270 280 290 300
GKTSATGVVF TRSPSTGEKK LFGEFLINAQ GEDIVSGTRT PMPIIANDSN
310 320 330 340 350
SMQAMMPEVF TKLSQIAKKL EEHYLDMQDI EFTIENNKLY ILQTRTAKRT
360 370 380 390 400
AIAAINIAVQ MVEEKLISKE QALMRIDPES LNQLLHTRID YSKKLTAIAE
410 420 430 440 450
GLPASPGAAT GIVVFSPYDA EKLSHHHKVI LVRHDTSPED INGMHVASGI
460 470 480 490 500
LTIRGGMTSH AAVVARGMGK PCVCGTNNLS IDEQKQILIA GDIVIKQGDI
510 520 530 540 550
ITIDGGSGKI FLGEMPLIQP TFSEESTLIL DWADEISSLK VRANAETVND
560 570 580 590 600
ALVSIKFGAQ GIGLCRSEHM FFDKNKIPLV REMIIAPDIE RRQCALQKLL
610 620 630 640 650
PLQTEDFKAL FRVMKNKPVN IRLLDPPLHE FLPTTDEDKK NLAHSLNLPL
660 670 680 690 700
SMIHQRLHAM HEVNPMLGHR GCRLGICLPE IYQMQIEAIL TAIFELHKKE
710 720 730 740 750
HIESNLELMI PLISNVAEIK KLKMDIYAVV KKLEQRYSYK FSFTLGTMIE
760 770 780 790 800
LPRAALGSKK IAKEVDYFSF GTNDLTQTTY GISRDDIASF LPYYLEEKIF
810 820 830 840 850
ESDPFTTLDE EGVGELIKIA IKRGKSSNAN LKLGACGEHA GNPTSIAFFH
860 870 880
KMNLNYVSCS PYRIPIARIA AAQAKIKQGS
Length:880
Mass (Da):98,165
Last modified:October 11, 2004 - v1
Checksum:iFFFE55AEEA138B34
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017197 Genomic DNA. Translation: AAU03950.1.
RefSeqiYP_067432.1. NC_006142.1.

Genome annotation databases

EnsemblBacteriaiAAU03950; AAU03950; RT0478.
KEGGirty:RT0478.
PATRICi17910198. VBIRicTyp34752_0507.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017197 Genomic DNA. Translation: AAU03950.1.
RefSeqiYP_067432.1. NC_006142.1.

3D structure databases

ProteinModelPortaliQ68WP2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi257363.RT0478.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAU03950; AAU03950; RT0478.
KEGGirty:RT0478.
PATRICi17910198. VBIRicTyp34752_0507.

Phylogenomic databases

eggNOGiCOG0574.
HOGENOMiHOG000039664.
KOiK01006.
OMAiVRRETNP.
OrthoDBiEOG6N0HGQ.

Enzyme and pathway databases

BioCyciRTYP257363:GJEQ-501-MONOMER.

Family and domain databases

Gene3Di3.20.20.60. 1 hit.
3.30.1490.20. 2 hits.
3.30.470.20. 1 hit.
3.50.30.10. 1 hit.
InterProiIPR013815. 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]
PANTHERiPTHR22931:SF9. PTHR22931:SF9. 1 hit.
PfamiPF00391. PEP-utilizers. 1 hit.
PF02896. PEP-utilizers_C. 1 hit.
PF01326. PPDK_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000853. PPDK. 1 hit.
SUPFAMiSSF51621. SSF51621. 1 hit.
SSF52009. SSF52009. 1 hit.
TIGRFAMsiTIGR01828. pyru_phos_dikin. 1 hit.
PROSITEiPS00742. PEP_ENZYMES_2. 1 hit.
PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC VR-144 / Wilmington.

Entry informationi

Entry nameiPPDK_RICTY
AccessioniPrimary (citable) accession number: Q68WP2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 29, 2007
Last sequence update: October 11, 2004
Last modified: April 29, 2015
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

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.

Keywords - Technical termi

Complete proteome

Documents

  1. Rickettsia typhi
    Rickettsia typhi (strain Wilmington): entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.