PPDK_CLOSY
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 03-AUG-2022, entry version 143.
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; Firmicutes; 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}.
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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 STRING; 742741.HMPREF9475_01824; -.
DR DrugBank; DB02522; Phosphonopyruvate.
DR PRIDE; P22983; -.
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; 3.20.20.60; -; 1.
DR Gene3D; 3.30.1490.20; -; 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 PANTHER; PTHR22931; PTHR22931; 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; SSF51621; SSF51621; 1.
DR SUPFAM; SSF52009; SSF52009; 1.
DR TIGRFAMs; TIGR01828; pyru_phos_dikin; 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
