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Protein

Pyruvate, phosphate dikinase

Gene

ppdK

Organism
Clostridium symbiosum (Bacteroides symbiosus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible phosphorylation of pyruvate and phosphate. In E.histolytica and C.symbiosus, PPDK functions in the direction of ATP synthesis.

Catalytic activityi

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

Cofactori

Mg2+1 Publication

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)DescriptionActionsGraphical viewLength
Binding sitei92ATPSequence analysis1
Active sitei455Tele-phosphohistidine intermediate1 Publication1
Binding sitei561Substrate1 Publication1
Binding sitei617Substrate1 Publication1
Metal bindingi745Magnesium1 Publication1
Binding sitei745Substrate1 Publication1
Binding sitei766Substrate; via carbonyl oxygen1 Publication1
Binding sitei767Substrate; via amide nitrogen1 Publication1
Binding sitei768Substrate1 Publication1
Metal bindingi769Magnesium1 Publication1
Binding sitei769Substrate; via amide nitrogen1 Publication1
Active sitei831Proton donor2 Publications1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Ligandi

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

Enzyme and pathway databases

BRENDAi2.7.9.1. 772.
SABIO-RKP22983.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvate, phosphate dikinase (EC:2.7.9.11 Publication)
Alternative name(s):
Pyruvate, orthophosphate dikinase
Gene namesi
Name:ppdK
OrganismiClostridium symbiosum (Bacteroides symbiosus)
Taxonomic identifieri1512 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesLachnospiraceae

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi831C → A: Lack of phosphotransfer activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001470462 – 874Pyruvate, phosphate dikinaseAdd BLAST873

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei453Phosphothreonine; by PDRP1By similarity1

Post-translational modificationi

Phosphorylation of Thr-453 in the dark inactivates the enzyme. Dephosphorylation upon light stimulation reactivates the enzyme (By similarity).By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PRIDEiP22983.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi742740.HMPREF9474_00893.

Structurei

Secondary structure

1874
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 7Combined sources3
Helixi8 – 10Combined sources3
Helixi13 – 15Combined sources3
Helixi16 – 31Combined sources16
Beta strandi39 – 42Combined sources4
Helixi44 – 51Combined sources8
Turni52 – 54Combined sources3
Helixi59 – 76Combined sources18
Beta strandi78 – 80Combined sources3
Beta strandi83 – 85Combined sources3
Beta strandi89 – 94Combined sources6
Turni100 – 102Combined sources3
Beta strandi105 – 109Combined sources5
Helixi115 – 123Combined sources9
Helixi126 – 144Combined sources19
Helixi149 – 162Combined sources14
Helixi168 – 170Combined sources3
Helixi173 – 188Combined sources16
Turni189 – 193Combined sources5
Helixi200 – 214Combined sources15
Helixi218 – 226Combined sources9
Helixi231 – 233Combined sources3
Beta strandi236 – 241Combined sources6
Beta strandi252 – 259Combined sources8
Turni261 – 263Combined sources3
Beta strandi266 – 275Combined sources10
Helixi278 – 283Combined sources6
Beta strandi284 – 286Combined sources3
Helixi291 – 293Combined sources3
Helixi294 – 297Combined sources4
Helixi299 – 316Combined sources18
Beta strandi320 – 327Combined sources8
Beta strandi330 – 338Combined sources9
Helixi343 – 355Combined sources13
Beta strandi357 – 359Combined sources3
Helixi361 – 367Combined sources7
Helixi370 – 377Combined sources8
Helixi383 – 388Combined sources6
Beta strandi391 – 394Combined sources4
Beta strandi396 – 399Combined sources4
Beta strandi401 – 410Combined sources10
Helixi411 – 419Combined sources9
Beta strandi424 – 430Combined sources7
Helixi433 – 435Combined sources3
Helixi436 – 441Combined sources6
Beta strandi443 – 449Combined sources7
Beta strandi452 – 454Combined sources3
Helixi455 – 463Combined sources9
Beta strandi466 – 469Combined sources4
Beta strandi475 – 477Combined sources3
Turni478 – 481Combined sources4
Beta strandi482 – 485Combined sources4
Beta strandi488 – 491Combined sources4
Beta strandi495 – 499Combined sources5
Turni500 – 502Combined sources3
Beta strandi504 – 508Combined sources5
Helixi519 – 531Combined sources13
Beta strandi534 – 539Combined sources6
Helixi543 – 551Combined sources9
Beta strandi556 – 560Combined sources5
Helixi564 – 567Combined sources4
Helixi569 – 580Combined sources12
Helixi584 – 592Combined sources9
Helixi595 – 609Combined sources15
Beta strandi614 – 617Combined sources4
Helixi623 – 626Combined sources4
Helixi631 – 641Combined sources11
Helixi645 – 655Combined sources11
Helixi660 – 662Combined sources3
Helixi667 – 672Combined sources6
Helixi674 – 695Combined sources22
Beta strandi702 – 705Combined sources4
Helixi711 – 732Combined sources22
Beta strandi739 – 744Combined sources6
Helixi747 – 751Combined sources5
Helixi753 – 756Combined sources4
Turni757 – 759Combined sources3
Beta strandi761 – 765Combined sources5
Helixi767 – 775Combined sources9
Helixi779 – 791Combined sources13
Turni799 – 801Combined sources3
Turni805 – 807Combined sources3
Helixi808 – 822Combined sources15
Beta strandi827 – 830Combined sources4
Helixi833 – 836Combined sources4
Helixi838 – 846Combined sources9
Beta strandi850 – 854Combined sources5
Helixi856 – 858Combined sources3
Helixi859 – 872Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DIKX-ray2.30A1-874[»]
1GGOX-ray2.60A2-874[»]
1JDEX-ray2.80A2-874[»]
1KBLX-ray1.94A2-874[»]
1KC7X-ray2.20A2-874[»]
2DIKX-ray2.50A2-874[»]
2FM4NMR-A384-511[»]
2R82X-ray3.60A1-874[»]
ProteinModelPortaliP22983.
SMRiP22983.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22983.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 340N-terminalAdd BLAST339
Regioni340 – 399Linker 1Add BLAST60
Regioni400 – 498CentralAdd BLAST99
Regioni499 – 533Linker 2Add BLAST35
Regioni534 – 874C-terminalAdd BLAST341

Domaini

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

Sequence similaritiesi

Belongs to the PEP-utilizing enzyme family.Curated

Phylogenomic databases

eggNOGiENOG4108HRN. Bacteria.
COG0574. LUCA.

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. 2 hits.
[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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P22983-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKWVYKFEE GNASMRNLLG GKGCNLAEMT ILGMPIPQGF TVTTEACTEY
60 70 80 90 100
YNSGKQITQE IQDQIFEAIT WLEELNGKKF GDTEDPLLVS VRSGARASMP
110 120 130 140 150
GMMDTILNLG LNDVAVEGFA KKTGNPRFAY DSYRRFIQMY SDVVMEVPKS
160 170 180 190 200
HFEKIIDAMK EEKGVHFDTD LTADDLKELA EKFKAVYKEA MNGEEFPQEP
210 220 230 240 250
KDQLMGAVKA VFRSWDNPRA IVYRRMNDIP GDWGTAVNVQ TMVFGNKGET
260 270 280 290 300
SGTGVAFTRN PSTGEKGIYG EYLINAQGED VVAGVRTPQP ITQLENDMPD
310 320 330 340 350
CYKQFMDLAM KLEKHFRDMQ DMEFTIEEGK LYFLQTRNGK RTAPAALQIA
360 370 380 390 400
CDLVDEGMIT EEEAVVRIEA KSLDQLLHPT FNPAALKAGE VIGSALPASP
410 420 430 440 450
GAAAGKVYFT ADEAKAAHEK GERVILVRLE TSPEDIEGMH AAEGILTVRG
460 470 480 490 500
GMTSHAAVVA RGMGTCCVSG CGEIKINEEA KTFELGGHTF AEGDYISLDG
510 520 530 540 550
STGKIYKGDI ETQEASVSGS FERIMVWADK FRTLKVRTNA DTPEDTLNAV
560 570 580 590 600
KLGAEGIGLC RTEHMFFEAD RIMKIRKMIL SDSVEAREEA LNELIPFQKG
610 620 630 640 650
DFKAMYKALE GRPMTVRYLD PPLHEFVPHT EEEQAELAKN MGLTLAEVKA
660 670 680 690 700
KVDELHEFNP MMGHRGCRLA VTYPEIAKMQ TRAVMEAAIE VKEETGIDIV
710 720 730 740 750
PEIMIPLVGE KKELKFVKDV VVEVAEQVKK EKGSDMQYHI GTMIEIPRAA
760 770 780 790 800
LTADAIAEEA EFFSFGTNDL TQMTFGFSRD DAGKFLDSYY KAKIYESDPF
810 820 830 840 850
ARLDQTGVGQ LVEMAVKKGR QTRPGLKCGI CGEHGGDPSS VEFCHKVGLN
860 870
YVSCSPFRVP IARLAAAQAA LNNK
Length:874
Mass (Da):96,654
Last modified:January 23, 2007 - v5
Checksum:i13C1918807DEA36C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti94G → A in AAA22917 (PubMed:2176881).Curated1
Sequence conflicti515A → R in AAA22917 (PubMed:2176881).Curated1
Sequence conflicti836 – 874GDPSS…ALNNK → EILLP in AAA22917 (PubMed:2176881).CuratedAdd BLAST39

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60920 mRNA. Translation: AAA22917.1.
PIRiA36231. KIQAPO.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60920 mRNA. Translation: AAA22917.1.
PIRiA36231. KIQAPO.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DIKX-ray2.30A1-874[»]
1GGOX-ray2.60A2-874[»]
1JDEX-ray2.80A2-874[»]
1KBLX-ray1.94A2-874[»]
1KC7X-ray2.20A2-874[»]
2DIKX-ray2.50A2-874[»]
2FM4NMR-A384-511[»]
2R82X-ray3.60A1-874[»]
ProteinModelPortaliP22983.
SMRiP22983.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi742740.HMPREF9474_00893.

Proteomic databases

PRIDEiP22983.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4108HRN. Bacteria.
COG0574. LUCA.

Enzyme and pathway databases

BRENDAi2.7.9.1. 772.
SABIO-RKP22983.

Miscellaneous databases

EvolutionaryTraceiP22983.

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. 2 hits.
[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...

Entry informationi

Entry nameiPPDK_CLOSY
AccessioniPrimary (citable) accession number: P22983
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 120 of the entry and version 5 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

3D-structure, Direct protein sequencing

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.