ID PPDK_CLOSY Reviewed; 874 AA. AC P22983; DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot. DT 23-JAN-2007, sequence version 5. DT 24-JAN-2024, entry version 149. DE RecName: Full=Pyruvate, phosphate dikinase; DE EC=2.7.9.1 {ECO:0000269|PubMed:7857929}; DE AltName: Full=Pyruvate, orthophosphate dikinase; GN Name=ppdK; OS Clostridium symbiosum (Bacteroides symbiosus). OC Bacteria; Bacillota; Clostridia; Eubacteriales; Lachnospiraceae. OX NCBI_TaxID=1512; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-11; 56-70; RP 128-134; 226-243; 372-386; 407-415; 652-664 AND 693-702. RX PubMed=2176881; DOI=10.1021/bi00500a006; RA Pocalyko D.J., Carroll L.J., Martin B.M., Babbitt P.C., Dunaway-Mariano D.; RT "Analysis of sequence homologies in plant and bacterial pyruvate phosphate RT dikinase, enzyme I of the bacterial phosphoenolpyruvate: sugar RT phosphotransferase system and other PEP-utilizing enzymes. Identification RT of potential catalytic and regulatory motifs."; RL Biochemistry 29:10757-10765(1990). RN [2] RP SEQUENCE REVISION TO 94. RA Dunaway-Mariano D., Ye D.; RL Submitted (SEP-2000) to UniProtKB. RN [3] RP PROTEIN SEQUENCE OF 451-462. RX PubMed=6257292; DOI=10.1021/bi00566a022; RA Goss N.H., Evans C.T., Wood H.G.; RT "Pyruvate phosphate dikinase: sequence of the histidyl peptide, the RT pyrophosphoryl and phosphoryl carrier."; RL Biochemistry 19:5805-5809(1980). RN [4] RP CATALYTIC ACTIVITY, ACTIVE SITE CYS-831, AND MUTAGENESIS OF CYS-831. RX PubMed=7857929; DOI=10.1021/bi00007a011; RA Xu Y., Yankie L., Shen L., Jung Y.S., Mariano P.S., Dunaway-Mariano D., RA Martin B.M.; RT "Location of the catalytic site for phosphoenolpyruvate formation within RT the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. RT 1. Identification of an essential cysteine by chemical modification with RT [1-14C]bromopyruvate and site-directed mutagenesis."; RL Biochemistry 34:2181-2187(1995). RN [5] RP STRUCTURE. RX PubMed=11695893; DOI=10.1021/bi0113061; RA Wei M., Ye D., Dunaway-Mariano D.; RT "Investigation of the role of the domain linkers in separate site catalysis RT by Clostridium symbiosum pyruvate phosphate dikinase."; RL Biochemistry 40:13466-13473(2001). RN [6] RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), AND ACTIVE SITE HIS-455. RX PubMed=11468288; DOI=10.1074/jbc.m105631200; RA Ye D., Wei M., McGuire M., Huang K., Kapadia G., Herzberg O., Martin B.M., RA Dunaway-Mariano D.; RT "Investigation of the catalytic site within the ATP-grasp domain of RT Clostridium symbiosum pyruvate phosphate dikinase."; RL J. Biol. Chem. 276:37630-37639(2001). RN [7] RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, RP SEQUENCE REVISION, ACTIVE SITE CYS-831, SUBSTRATE BINDING AT ARG-561; RP ARG-617; GLU-745; GLY-766; THR-767; ASN-768 AND ASP-769, METAL BINDING AT RP GLU-745 AND ASP-769, AND COFACTOR. RX PubMed=8610096; DOI=10.1073/pnas.93.7.2652; RA Herzberg O., Cheng C.C.H., Kapadia G., McGuire M., Carroll L.J., Noh S.J., RA Dunaway-Mariano D.; RT "Swiveling-domain mechanism for enzymatic phosphotransfer between remote RT reaction sites."; RL Proc. Natl. Acad. Sci. U.S.A. 93:2652-2657(1996). RN [8] RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS). RC STRAIN=JM101; RX PubMed=9753432; DOI=10.1021/bi980920i; RA McGuire M., Huang K., Kapadia G., Herzberg O., Dunaway-Mariano D.; RT "Location of the phosphate binding site within Clostridium symbiosum RT pyruvate phosphate dikinase."; RL Biochemistry 37:13463-13474(1998). CC -!- FUNCTION: Catalyzes the reversible phosphorylation of pyruvate and CC phosphate. In E.histolytica and C.symbiosus, PPDK functions in the CC direction of ATP synthesis. CC -!- CATALYTIC ACTIVITY: CC Reaction=ATP + phosphate + pyruvate = AMP + diphosphate + H(+) + CC phosphoenolpyruvate; Xref=Rhea:RHEA:10756, ChEBI:CHEBI:15361, CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58702, ChEBI:CHEBI:456215; EC=2.7.9.1; CC -!- COFACTOR: CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; CC Evidence={ECO:0000269|PubMed:8610096}; CC -!- ACTIVITY REGULATION: Activated by light-induced dephosphorylation. CC Inhibited by dark-induced phosphorylation. Both reactions are catalyzed CC by PDRP1 (By similarity). {ECO:0000250}. CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:8610096}. CC -!- DOMAIN: The N-terminal domain contains the ATP/Pi binding site, the CC central domain the pyrophosphate/phosphate carrier histidine, and the CC C-terminal domain the pyruvate binding site. CC -!- PTM: Phosphorylation of Thr-453 in the dark inactivates the enzyme. CC Dephosphorylation upon light stimulation reactivates the enzyme (By CC similarity). {ECO:0000250}. CC -!- MISCELLANEOUS: The reaction takes place in three steps, each mediated CC by a carrier histidine residue located on the surface of the central CC domain. The two first partial reactions are catalyzed at an active site CC located on the N-terminal domain, and the third partial reaction is CC catalyzed at an active site located on the C-terminal domain. For CC catalytic turnover, the central domain swivels from the concave surface CC of the N-terminal domain to that of the C-terminal domain. CC -!- SIMILARITY: Belongs to the PEP-utilizing enzyme family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; M60920; AAA22917.1; -; mRNA. DR PIR; A36231; KIQAPO. DR PDB; 1DIK; X-ray; 2.30 A; A=1-874. DR PDB; 1GGO; X-ray; 2.60 A; A=2-874. DR PDB; 1JDE; X-ray; 2.80 A; A=2-874. DR PDB; 1KBL; X-ray; 1.94 A; A=2-874. DR PDB; 1KC7; X-ray; 2.20 A; A=2-874. DR PDB; 2DIK; X-ray; 2.50 A; A=2-874. DR PDB; 2FM4; NMR; -; A=384-511. DR PDB; 2R82; X-ray; 3.60 A; A=1-874. DR PDBsum; 1DIK; -. DR PDBsum; 1GGO; -. DR PDBsum; 1JDE; -. DR PDBsum; 1KBL; -. DR PDBsum; 1KC7; -. DR PDBsum; 2DIK; -. DR PDBsum; 2FM4; -. DR PDBsum; 2R82; -. DR AlphaFoldDB; P22983; -. DR BMRB; P22983; -. DR SMR; P22983; -. DR DrugBank; DB02522; Phosphonopyruvate. DR eggNOG; COG0574; Bacteria. DR eggNOG; COG1080; Bacteria. DR BRENDA; 2.7.9.1; 772. DR SABIO-RK; P22983; -. DR EvolutionaryTrace; P22983; -. DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW. DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0050242; F:pyruvate, phosphate dikinase activity; IEA:UniProtKB-EC. DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW. DR GO; GO:0006090; P:pyruvate metabolic process; IEA:InterPro. DR Gene3D; 1.20.80.30; -; 1. DR Gene3D; 3.30.1490.20; ATP-grasp fold, A domain; 1. DR Gene3D; 3.30.470.20; ATP-grasp fold, B domain; 1. DR Gene3D; 3.20.20.60; Phosphoenolpyruvate-binding domains; 1. DR Gene3D; 3.50.30.10; Phosphohistidine domain; 1. DR Gene3D; 1.10.189.10; Pyruvate Phosphate Dikinase, domain 2; 1. DR InterPro; IPR013815; ATP_grasp_subdomain_1. DR InterPro; IPR008279; PEP-util_enz_mobile_dom. DR InterPro; IPR018274; PEP_util_AS. DR InterPro; IPR000121; PEP_util_C. DR InterPro; IPR023151; PEP_util_CS. DR InterPro; IPR036637; Phosphohistidine_dom_sf. DR InterPro; IPR002192; PPDK_AMP/ATP-bd. DR InterPro; IPR010121; Pyruvate_phosphate_dikinase. DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom. DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf. DR NCBIfam; TIGR01828; pyru_phos_dikin; 1. DR PANTHER; PTHR22931; PHOSPHOENOLPYRUVATE DIKINASE-RELATED; 1. DR PANTHER; PTHR22931:SF9; PYRUVATE, PHOSPHATE DIKINASE 1, CHLOROPLASTIC; 1. DR Pfam; PF00391; PEP-utilizers; 1. DR Pfam; PF02896; PEP-utilizers_C; 1. DR Pfam; PF01326; PPDK_N; 2. DR PIRSF; PIRSF000853; PPDK; 1. DR SUPFAM; SSF56059; Glutathione synthetase ATP-binding domain-like; 1. DR SUPFAM; SSF51621; Phosphoenolpyruvate/pyruvate domain; 1. DR SUPFAM; SSF52009; Phosphohistidine domain; 1. DR PROSITE; PS00742; PEP_ENZYMES_2; 1. DR PROSITE; PS00370; PEP_ENZYMES_PHOS_SITE; 1. PE 1: Evidence at protein level; KW 3D-structure; ATP-binding; Direct protein sequencing; Kinase; Magnesium; KW Metal-binding; Nucleotide-binding; Phosphoprotein; Transferase. FT INIT_MET 1 FT /note="Removed" FT /evidence="ECO:0000269|PubMed:2176881" FT CHAIN 2..874 FT /note="Pyruvate, phosphate dikinase" FT /id="PRO_0000147046" FT REGION 2..340 FT /note="N-terminal" FT REGION 340..399 FT /note="Linker 1" FT REGION 400..498 FT /note="Central" FT REGION 499..533 FT /note="Linker 2" FT REGION 534..874 FT /note="C-terminal" FT ACT_SITE 455 FT /note="Tele-phosphohistidine intermediate" FT /evidence="ECO:0000269|PubMed:11468288" FT ACT_SITE 831 FT /note="Proton donor" FT /evidence="ECO:0000305|PubMed:7857929, FT ECO:0000305|PubMed:8610096" FT BINDING 92 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255" FT BINDING 561 FT /ligand="substrate" FT /evidence="ECO:0000269|PubMed:8610096" FT BINDING 617 FT /ligand="substrate" FT /evidence="ECO:0000269|PubMed:8610096" FT BINDING 745 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /evidence="ECO:0000269|PubMed:8610096" FT BINDING 745 FT /ligand="substrate" FT /evidence="ECO:0000269|PubMed:8610096" FT BINDING 766 FT /ligand="substrate" FT /evidence="ECO:0000269|PubMed:8610096" FT BINDING 767 FT /ligand="substrate" FT /evidence="ECO:0000269|PubMed:8610096" FT BINDING 768 FT /ligand="substrate" FT /evidence="ECO:0000269|PubMed:8610096" FT BINDING 769 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /evidence="ECO:0000269|PubMed:8610096" FT BINDING 769 FT /ligand="substrate" FT /evidence="ECO:0000269|PubMed:8610096" FT MOD_RES 453 FT /note="Phosphothreonine; by PDRP1" FT /evidence="ECO:0000250" FT MUTAGEN 831 FT /note="C->A: Lack of phosphotransfer activity." FT /evidence="ECO:0000269|PubMed:7857929" FT CONFLICT 94 FT /note="G -> A (in Ref. 1; AAA22917)" FT /evidence="ECO:0000305" FT CONFLICT 515 FT /note="A -> R (in Ref. 1; AAA22917)" FT /evidence="ECO:0000305" FT CONFLICT 836..874 FT /note="GDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNNK -> EILLP (in FT Ref. 1; AAA22917)" FT /evidence="ECO:0000305" FT STRAND 5..7 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 8..10 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 13..15 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 16..31 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 39..42 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 44..51 FT /evidence="ECO:0007829|PDB:1KBL" FT TURN 52..54 FT /evidence="ECO:0007829|PDB:1KC7" FT HELIX 59..76 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 78..80 FT /evidence="ECO:0007829|PDB:1KC7" FT STRAND 83..85 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 89..94 FT /evidence="ECO:0007829|PDB:1KBL" FT TURN 100..102 FT /evidence="ECO:0007829|PDB:1KC7" FT STRAND 105..109 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 115..123 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 126..144 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 149..162 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 168..170 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 173..188 FT /evidence="ECO:0007829|PDB:1KBL" FT TURN 189..193 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 200..214 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 218..226 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 231..233 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 236..241 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 252..259 FT /evidence="ECO:0007829|PDB:1KBL" FT TURN 261..263 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 266..275 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 278..283 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 284..286 FT /evidence="ECO:0007829|PDB:1JDE" FT HELIX 291..293 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 294..297 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 299..316 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 320..327 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 330..338 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 343..355 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 357..359 FT /evidence="ECO:0007829|PDB:1GGO" FT HELIX 361..367 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 370..377 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 383..388 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 391..394 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 396..399 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 401..410 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 411..419 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 424..430 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 433..435 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 436..441 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 443..449 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 452..454 FT /evidence="ECO:0007829|PDB:1JDE" FT HELIX 455..463 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 466..469 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 475..477 FT /evidence="ECO:0007829|PDB:1KBL" FT TURN 478..481 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 482..485 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 488..491 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 495..499 FT /evidence="ECO:0007829|PDB:1KBL" FT TURN 500..502 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 504..508 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 519..531 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 534..539 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 543..551 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 556..560 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 564..567 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 569..580 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 584..592 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 595..609 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 614..617 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 623..626 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 631..641 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 645..655 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 660..662 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 667..672 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 674..695 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 702..705 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 711..732 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 739..744 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 747..751 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 753..756 FT /evidence="ECO:0007829|PDB:1KBL" FT TURN 757..759 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 761..765 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 767..775 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 779..791 FT /evidence="ECO:0007829|PDB:1KBL" FT TURN 799..801 FT /evidence="ECO:0007829|PDB:1KBL" FT TURN 805..807 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 808..822 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 827..830 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 833..836 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 838..846 FT /evidence="ECO:0007829|PDB:1KBL" FT STRAND 850..854 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 856..858 FT /evidence="ECO:0007829|PDB:1KBL" FT HELIX 859..872 FT /evidence="ECO:0007829|PDB:1KBL" SQ SEQUENCE 874 AA; 96654 MW; 13C1918807DEA36C CRC64; MAKWVYKFEE GNASMRNLLG GKGCNLAEMT ILGMPIPQGF TVTTEACTEY YNSGKQITQE IQDQIFEAIT WLEELNGKKF GDTEDPLLVS VRSGARASMP GMMDTILNLG LNDVAVEGFA KKTGNPRFAY DSYRRFIQMY SDVVMEVPKS HFEKIIDAMK EEKGVHFDTD LTADDLKELA EKFKAVYKEA MNGEEFPQEP KDQLMGAVKA VFRSWDNPRA IVYRRMNDIP GDWGTAVNVQ TMVFGNKGET SGTGVAFTRN PSTGEKGIYG EYLINAQGED VVAGVRTPQP ITQLENDMPD CYKQFMDLAM KLEKHFRDMQ DMEFTIEEGK LYFLQTRNGK RTAPAALQIA CDLVDEGMIT EEEAVVRIEA KSLDQLLHPT FNPAALKAGE VIGSALPASP GAAAGKVYFT ADEAKAAHEK GERVILVRLE TSPEDIEGMH AAEGILTVRG GMTSHAAVVA RGMGTCCVSG CGEIKINEEA KTFELGGHTF AEGDYISLDG STGKIYKGDI ETQEASVSGS FERIMVWADK FRTLKVRTNA DTPEDTLNAV KLGAEGIGLC RTEHMFFEAD RIMKIRKMIL SDSVEAREEA LNELIPFQKG DFKAMYKALE GRPMTVRYLD PPLHEFVPHT EEEQAELAKN MGLTLAEVKA KVDELHEFNP MMGHRGCRLA VTYPEIAKMQ TRAVMEAAIE VKEETGIDIV PEIMIPLVGE KKELKFVKDV VVEVAEQVKK EKGSDMQYHI GTMIEIPRAA LTADAIAEEA EFFSFGTNDL TQMTFGFSRD DAGKFLDSYY KAKIYESDPF ARLDQTGVGQ LVEMAVKKGR QTRPGLKCGI CGEHGGDPSS VEFCHKVGLN YVSCSPFRVP IARLAAAQAA LNNK //