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P22983

- PPDK_CLOSY

UniProt

P22983 - PPDK_CLOSY

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Protein

Pyruvate, phosphate dikinase

Gene

ppdK

Organism
Clostridium symbiosum (Bacteroides symbiosus)
Status
Reviewed - 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

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 sitei92 – 921ATPSequence Analysis
Active sitei455 – 4551Tele-phosphohistidine intermediate1 Publication
Binding sitei561 – 5611Substrate
Binding sitei617 – 6171Substrate
Metal bindingi745 – 7451Magnesium
Binding sitei745 – 7451Substrate
Binding sitei766 – 7661Substrate; via carbonyl oxygen
Binding sitei767 – 7671Substrate; via amide nitrogen
Binding sitei768 – 7681Substrate
Metal bindingi769 – 7691Magnesium
Binding sitei769 – 7691Substrate; via amide nitrogen
Active sitei831 – 8311Proton donor2 Publications

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

BioCyciRETL1328306-WGS:GSTH-1025-MONOMER.
SABIO-RKP22983.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvate, phosphate dikinase (EC:2.7.9.1)
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi831 – 8311C → A: Lack of phosphotransfer activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 874873Pyruvate, phosphate dikinasePRO_0000147046Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei453 – 4531Phosphothreonine; by PDRP1By similarity

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

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

Secondary structure

1
874
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 73Combined sources
Helixi8 – 103Combined sources
Helixi13 – 153Combined sources
Helixi16 – 3116Combined sources
Beta strandi39 – 424Combined sources
Helixi44 – 518Combined sources
Turni52 – 543Combined sources
Helixi59 – 7618Combined sources
Beta strandi78 – 803Combined sources
Beta strandi83 – 853Combined sources
Beta strandi89 – 946Combined sources
Turni100 – 1023Combined sources
Beta strandi105 – 1095Combined sources
Helixi115 – 1239Combined sources
Helixi126 – 14419Combined sources
Helixi149 – 16214Combined sources
Helixi168 – 1703Combined sources
Helixi173 – 18816Combined sources
Turni189 – 1935Combined sources
Helixi200 – 21415Combined sources
Helixi218 – 2269Combined sources
Helixi231 – 2333Combined sources
Beta strandi236 – 2416Combined sources
Beta strandi252 – 2598Combined sources
Turni261 – 2633Combined sources
Beta strandi266 – 27510Combined sources
Helixi278 – 2836Combined sources
Beta strandi284 – 2863Combined sources
Helixi291 – 2933Combined sources
Helixi294 – 2974Combined sources
Helixi299 – 31618Combined sources
Beta strandi320 – 3278Combined sources
Beta strandi330 – 3389Combined sources
Helixi343 – 35513Combined sources
Beta strandi357 – 3593Combined sources
Helixi361 – 3677Combined sources
Helixi370 – 3778Combined sources
Helixi383 – 3886Combined sources
Beta strandi391 – 3944Combined sources
Beta strandi396 – 3994Combined sources
Beta strandi401 – 41010Combined sources
Helixi411 – 4199Combined sources
Beta strandi424 – 4307Combined sources
Helixi433 – 4353Combined sources
Helixi436 – 4416Combined sources
Beta strandi443 – 4497Combined sources
Beta strandi452 – 4543Combined sources
Helixi455 – 4639Combined sources
Beta strandi466 – 4694Combined sources
Beta strandi475 – 4773Combined sources
Turni478 – 4814Combined sources
Beta strandi482 – 4854Combined sources
Beta strandi488 – 4914Combined sources
Beta strandi495 – 4995Combined sources
Turni500 – 5023Combined sources
Beta strandi504 – 5085Combined sources
Helixi519 – 53113Combined sources
Beta strandi534 – 5396Combined sources
Helixi543 – 5519Combined sources
Beta strandi556 – 5605Combined sources
Helixi564 – 5674Combined sources
Helixi569 – 58012Combined sources
Helixi584 – 5929Combined sources
Helixi595 – 60915Combined sources
Beta strandi614 – 6174Combined sources
Helixi623 – 6264Combined sources
Helixi631 – 64111Combined sources
Helixi645 – 65511Combined sources
Helixi660 – 6623Combined sources
Helixi667 – 6726Combined sources
Helixi674 – 69522Combined sources
Beta strandi702 – 7054Combined sources
Helixi711 – 73222Combined sources
Beta strandi739 – 7446Combined sources
Helixi747 – 7515Combined sources
Helixi753 – 7564Combined sources
Turni757 – 7593Combined sources
Beta strandi761 – 7655Combined sources
Helixi767 – 7759Combined sources
Helixi779 – 79113Combined sources
Turni799 – 8013Combined sources
Turni805 – 8073Combined sources
Helixi808 – 82215Combined sources
Beta strandi827 – 8304Combined sources
Helixi833 – 8364Combined sources
Helixi838 – 8469Combined sources
Beta strandi850 – 8545Combined sources
Helixi856 – 8583Combined sources
Helixi859 – 87214Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 2-873.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22983.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni2 – 340339N-terminalAdd
BLAST
Regioni340 – 39960Linker 1Add
BLAST
Regioni400 – 49899CentralAdd
BLAST
Regioni499 – 53335Linker 2Add
BLAST
Regioni534 – 874341C-terminalAdd
BLAST

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

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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti94 – 941G → A in AAA22917. (PubMed:2176881)Curated
Sequence conflicti515 – 5151A → R in AAA22917. (PubMed:2176881)Curated
Sequence conflicti836 – 87439GDPSS…ALNNK → EILLP in AAA22917. (PubMed:2176881)CuratedAdd
BLAST

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 .
PIRi A36231. KIQAPO.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1DIK X-ray 2.30 A 1-874 [» ]
1GGO X-ray 2.60 A 2-874 [» ]
1JDE X-ray 2.80 A 2-874 [» ]
1KBL X-ray 1.94 A 2-874 [» ]
1KC7 X-ray 2.20 A 2-874 [» ]
2DIK X-ray 2.50 A 2-874 [» ]
2FM4 NMR - A 384-511 [» ]
2R82 X-ray 3.60 A 1-874 [» ]
ProteinModelPortali P22983.
SMRi P22983. Positions 2-873.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

BioCyci RETL1328306-WGS:GSTH-1025-MONOMER.
SABIO-RK P22983.

Miscellaneous databases

EvolutionaryTracei P22983.

Family and domain databases

Gene3Di 3.20.20.60. 1 hit.
3.30.1490.20. 2 hits.
3.30.470.20. 1 hit.
3.50.30.10. 1 hit.
InterProi IPR013815. 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 ]
PANTHERi PTHR22931:SF9. PTHR22931:SF9. 1 hit.
Pfami PF00391. PEP-utilizers. 1 hit.
PF02896. PEP-utilizers_C. 1 hit.
PF01326. PPDK_N. 1 hit.
[Graphical view ]
PIRSFi PIRSF000853. PPDK. 1 hit.
SUPFAMi SSF51621. SSF51621. 1 hit.
SSF52009. SSF52009. 1 hit.
TIGRFAMsi TIGR01828. pyru_phos_dikin. 1 hit.
PROSITEi PS00742. PEP_ENZYMES_2. 1 hit.
PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs."
    Pocalyko D.J., Carroll L.J., Martin B.M., Babbitt P.C., Dunaway-Mariano D.
    Biochemistry 29:10757-10765(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-11; 56-70; 128-134; 226-243; 372-386; 407-415; 652-664 AND 693-702.
  2. Dunaway-Mariano D., Ye D.
    Submitted (SEP-2000) to UniProtKB
    Cited for: SEQUENCE REVISION TO 94.
  3. "Pyruvate phosphate dikinase: sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier."
    Goss N.H., Evans C.T., Wood H.G.
    Biochemistry 19:5805-5809(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 451-462.
  4. "Location of the catalytic site for phosphoenolpyruvate formation within the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. 1. Identification of an essential cysteine by chemical modification with [1-14C]bromopyruvate and site-directed mutagenesis."
    Xu Y., Yankie L., Shen L., Jung Y.S., Mariano P.S., Dunaway-Mariano D., Martin B.M.
    Biochemistry 34:2181-2187(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACTIVE SITE CYS-831, MUTAGENESIS OF CYS-831.
  5. "Investigation of the role of the domain linkers in separate site catalysis by Clostridium symbiosum pyruvate phosphate dikinase."
    Wei M., Ye D., Dunaway-Mariano D.
    Biochemistry 40:13466-13473(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE.
  6. "Investigation of the catalytic site within the ATP-grasp domain of Clostridium symbiosum pyruvate phosphate dikinase."
    Ye D., Wei M., McGuire M., Huang K., Kapadia G., Herzberg O., Martin B.M., Dunaway-Mariano D.
    J. Biol. Chem. 276:37630-37639(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), ACTIVE SITE HIS-455.
  7. "Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites."
    Herzberg O., Cheng C.C.H., Kapadia G., McGuire M., Carroll L.J., Noh S.J., Dunaway-Mariano D.
    Proc. Natl. Acad. Sci. U.S.A. 93:2652-2657(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SEQUENCE REVISION, ACTIVE SITE CYS-831, SUBSTRATE BINDING AT ARG-561; ARG-617; GLU-745; GLY-766; THR-767; ASN-768 AND ASP-769, METAL BINDING AT GLU-745 AND ASP-769.
  8. "Location of the phosphate binding site within Clostridium symbiosum pyruvate phosphate dikinase."
    McGuire M., Huang K., Kapadia G., Herzberg O., Dunaway-Mariano D.
    Biochemistry 37:13463-13474(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
    Strain: JM101.

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 26, 2014
This is version 111 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

External Data

Dasty 3