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(-) Description

Title :  CRYSTAL STRUCTURE OF POLYPHOSPHATE KINASE FROM PORPHYROMONAS GINGIVALIS
 
Authors :  Y. Patskovsky, R. Toro, J. M. Sauder, M. Dickey, J. M. Adams, S. Ozyurt, S. R. Wasserman, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  12 Dec 06  (Deposition) - 19 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Structural Genomics, Protein Structure Initiative, Psi, Nysgrc, New York Structural Genomics Research Consortium, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, J. M. Sauder, M. Dickey, J. M. Adams, S. Ozyurt, S. R. Wasserman, S. K. Burley, S. C. Almo
Crystal Structure Of Polyphosphate Kinase From Porphyromonas Gingivalis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYPHOSPHATE KINASE
    Chains: A, B
    EC Number: 2.7.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: PPK
    Mutation: YES
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 837
    Strain: ATCC BAA-308 / W83

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 48)

Asymmetric/Biological Unit (2, 48)
No.NameCountTypeFull Name
1MSE35Mod. Amino AcidSELENOMETHIONINE
2SO413Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:114 , ARG B:116 , PRO B:120 , THR B:121 , HIS B:122BINDING SITE FOR RESIDUE SO4 B 704
02AC2SOFTWAREARG A:10 , ARG A:11 , LYS B:666BINDING SITE FOR RESIDUE SO4 A 704
03AC3SOFTWARESER A:44 , ASP A:93 , TYR A:96 , TYR A:97 , MSE A:268 , LEU A:301BINDING SITE FOR RESIDUE SO4 A 705
04AC4SOFTWAREHIS B:437 , HIS B:595 , ARG B:597BINDING SITE FOR RESIDUE SO4 B 705
05AC5SOFTWAREARG A:490 , ARG A:503BINDING SITE FOR RESIDUE SO4 A 706
06AC6SOFTWAREHIS A:437 , LYS A:439 , HIS A:595 , ARG A:597BINDING SITE FOR RESIDUE SO4 A 707
07AC7SOFTWARETHR A:468 , ALA A:469 , ARG A:470 , ARG B:415BINDING SITE FOR RESIDUE SO4 A 708
08AC8SOFTWAREARG A:114 , ARG A:116 , PRO A:120 , THR A:121 , HIS A:122 , ALA A:406BINDING SITE FOR RESIDUE SO4 A 709
09AC9SOFTWAREASP A:576 , MSE A:577 , PRO A:578 , ARG A:581 , ARG B:534 , GLU B:645BINDING SITE FOR RESIDUE SO4 B 706
10BC1SOFTWARELEU A:324 , ASP A:353 , ARG A:357 , ALA B:392 , GLN B:393BINDING SITE FOR RESIDUE SO4 A 710
11BC2SOFTWAREARG B:156 , ARG B:159BINDING SITE FOR RESIDUE SO4 B 707
12BC3SOFTWAREALA B:469 , ARG B:470 , TYR B:472BINDING SITE FOR RESIDUE SO4 B 708
13BC4SOFTWAREARG A:114 , LEU A:115 , ARG A:116 , THR A:117 , HIS A:118BINDING SITE FOR RESIDUE SO4 A 711

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O8R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O8R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O8R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O8R)

(-) Exons   (0, 0)

(no "Exon" information available for 2O8R)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:648
 aligned with Q7MTR1_PORGI | Q7MTR1 from UniProtKB/TrEMBL  Length:695

    Alignment length:688
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683        
         Q7MTR1_PORGI     4 SAYPFFRRDMSWLSFNERVLMEAADRTLPVYDRIKFLSIFSSNLEEFYTVRVAYHQAVLQKRRDRSEAEEDSDADAHILQAIRETVIRQDELYYRIFYDQILPTLEEHGIRLRTHAPTHPDHKAYLRRFFHEEIFPLLYPMLLLPSKVRTFIRSGRVYLAVRLKEKETDEAYSYALLNVPTDGLPRFVELPRLQTDTFYYYSFLEDIIKEHLDVVFPGYEVMDSYSIKVSRDADLLLDAQRPEDLPGEIRKKVKTRKLGAPTRFMYDGRMPDEVLRYICSSCDIDPEEAIRSGNYVNLQDLAMLPNPFAPRLETLTPEPLLSKHLEQAPSLMEGIRRKDYLIHVPYYTYDYVVRLLMEAAISPDVSEIRLTQYRVAENSSIISALEAAAQSGKKVSVFVELKARFDEENNLRLSERMRRSGIRIVYSMPGLKVHAKTALILYHTPAGERPQGIALLSTGNFNETTARIYSDTTLMTANTDIVHDVYRLFRILDGDPEPARFSRLLVARYNMGEAITNLIEREIENVKRGKRGYMLLKMNGLQDKNVITQLYRASEAGVEIDLIVRGICCLVPDMPQSRNIRVTRLVDMYLEHSRIWCFHNGGKEEVFISSADWMKRNLYNRIETACPVLDPALRREIIDILEIQLRDNIKACRIDSSLNNIYKHNSDEKPVRAQAAIYRYLKGKEEAT 691
               SCOP domains d2o8ra1 A:4-112 Polyphosphate kinase, PPK                                                                    d2o8ra2 A:113-317 Polyphosphate kinase, PPK                                                                                                                                                                  d2o8ra3 A:318-505 Polyphosphate kinase, PPK                                                                                                                                                 d2o8ra4 A:506-691 Polyphosphate kinase, PPK                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------               -------------------------------------------------------------------------------------------------------------------------------------------------------------------                     ----------------------------------------------------------2o8rA02 A:322-507 Endonuclease Chain A                                                                                                                                                    --2o8rA03 A:510-689 Endonuclease Chain A                                                                                                                                              -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhhhhhh..ee...............eeeeeee........eeeeee........eeee........eeeeehhhhhhhhhhhhh...eeeeeeeeeee.........---------------------..eeeee...hhhhhhhhh.........eeee....hhhhhhhh.................hhhhhh..hhhhhhhhh.eeeee.....hhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhh..eeeeee......----hhhhhhhhhhhh.eeee..........eeeeee.........eeeeee...........eeeeeeee.hhhhhhhhhhhhhhhh...........ee...hhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhh..eeeeee.........hhhhh.eeeee.....ee...eeee.hhhh.eeeee....hhhhhhh...eeee..hhhhhhhhhhhhhhhhhh....eee.....eee.........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o8r A   4 SAYPFFRRDmSWLSFNERVLmEAADRTLPVYDRIKFLSIFSSNLEEFYTVRVAYHQAVLQK---------------HILQAIRETVIRQDELYYRIFYDQILPTLEEHGIRLRTHAPTHPDHKAYLRRFFHEEIFPLLYPmLLLPSKVRTFIRSGRVYLAVRLKEKETDEAYSYALLNVPTDGLPRFVELPRLQTDTFYYYSFLEDIIKEHLDVVFPGYEVmDSYSIKVSRDADLLLDA---------------------PTRFmYDGRmPDEVLRYICSSCDIDPEEAIRSGNYVNLQDLAmLPNPFAPRLETLTPEPLLSKHLEQAPSLmEGIRRKDYLIHVPYYTYDYVVRLLmEAAISPDVSEIRLTQYRVAENSSIISALEAAAQSGKKVSVFVELKARF----NLRLSERmRRSGIRIVYSmPGLKVHAKTALILYHTPAGERPQGIALLSTGNFNETTARIYSDTTLmTANTDIVHDVYRLFRILDGDPEPARFSRLLVARYNmGEAITNLIEREIENVKRGKRGYmLLKmNGLQDKNVITQLYRASEAGVEIDLIVRGICCLVPDmPQSRNIRVTRLVDmYLEHSRIWCFHNGGKEEVFISSADWmKRNLYNRIETACPVLDPTLRREIIDILEIQLRDNIKACRIDSSLNNIYKHNSDEKPVRAQAAIYRYLKGKEETT 691
                                    13        23|       33        43        53        63|        -      | 83        93       103       113       123       133       143|      153       163       173       183       193       203       213       223 |     233        |-         -         -|   |  273       283       293       303  |    313       323       333 |     343       353      |363       373       383       393       403    |  413      |423       433       443       453       463       473    |  483       493       503       513|      523       533   |   543       553       563       573   |   583       593       603       613   |   623       633       643       653       663       673       683        
                                    13-MSE     24-MSE                                  64              80                                                             144-MSE                                                                          225-MSE          242                   264   |    |                              306-MSE                      335-MSE                  360-MSE                                         408  413      |        431-MSE                                        478-MSE                             514-MSE                537-MSE                                 577-MSE       591-MSE                   617-MSE                                                                      
                                                                                                                                                                                                                                                                                                  268-MSE|                                                                                                                                                420-MSE                                                                                                                  541-MSE                                                                                                                                                  
                                                                                                                                                                                                                                                                                                       273-MSE                                                                                                                                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:605
 aligned with Q7MTR1_PORGI | Q7MTR1 from UniProtKB/TrEMBL  Length:695

    Alignment length:680
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690
         Q7MTR1_PORGI    11 RDMSWLSFNERVLMEAADRTLPVYDRIKFLSIFSSNLEEFYTVRVAYHQAVLQKRRDRSEAEEDSDADAHILQAIRETVIRQDELYYRIFYDQILPTLEEHGIRLRTHAPTHPDHKAYLRRFFHEEIFPLLYPMLLLPSKVRTFIRSGRVYLAVRLKEKETDEAYSYALLNVPTDGLPRFVELPRLQTDTFYYYSFLEDIIKEHLDVVFPGYEVMDSYSIKVSRDADLLLDAQRPEDLPGEIRKKVKTRKLGAPTRFMYDGRMPDEVLRYICSSCDIDPEEAIRSGNYVNLQDLAMLPNPFAPRLETLTPEPLLSKHLEQAPSLMEGIRRKDYLIHVPYYTYDYVVRLLMEAAISPDVSEIRLTQYRVAENSSIISALEAAAQSGKKVSVFVELKARFDEENNLRLSERMRRSGIRIVYSMPGLKVHAKTALILYHTPAGERPQGIALLSTGNFNETTARIYSDTTLMTANTDIVHDVYRLFRILDGDPEPARFSRLLVARYNMGEAITNLIEREIENVKRGKRGYMLLKMNGLQDKNVITQLYRASEAGVEIDLIVRGICCLVPDMPQSRNIRVTRLVDMYLEHSRIWCFHNGGKEEVFISSADWMKRNLYNRIETACPVLDPALRREIIDILEIQLRDNIKACRIDSSLNNIYKHNSDEKPVRAQAAIYRYLKGKEEA 690
               SCOP domains d2o8rb1 B:11-112 Polyphosphate kinase, PPK                                                            d2o8rb2 B:113-317 Polyphosphate kinase, PPK                                                                                                                                                                  d2o8rb3 B:318-505 Polyphosphate kinase, PPK                                                                                                                                                 d2o8rb4 B:506-690 Polyphosphate kinase, PPK                                                                                                                                               SCOP domains
               CATH domains 2o8rB01 B:11-111,B:307-319 PPK N-terminal domai                        n-like domains                2o8rB02 B:112-305 polyphosphate kinase like                                                                                                                                                       -2o8rB01      2o8rB03 B:320-503,B:593-596 Endonuclease Chain A                                                                                                                                        2o8rB04 B:504-592,B:597-616,B:621-690 Endonuclease Chain A                               2o8r2o8rB04                 2o8rB04 B:504-592,B:597-616,B:621-6        90 Endonuclease Chain A     CATH domains
           Pfam domains (1) PP_kinase_N-2o8rB05 B:11-117                                                                               -----PP_kinase-2o8rB03 B:123-328                                                                                                                                                                                   ----PP_kinase_C-2o8rB01 B:333-685                                                                                                                                                                                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) PP_kinase_N-2o8rB06 B:11-117                                                                               -----PP_kinase-2o8rB04 B:123-328                                                                                                                                                                                   ----PP_kinase_C-2o8rB02 B:333-685                                                                                                                                                                                                                                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee......hhhhhhhhhhhhhhhhhhhh..ee..............eeeeeeee.hhhhh..eeeeee........eeee........eeeeehhhhhhhhhhhhh...eeeeeeeeeee.-----------------------------..eeeee...hhhhhh..----------..ee....hhhhhhh..................hhhhhh..hhhhhhhhh.eeee.....hhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhh.eeee.........eeeeeee.........eeeeee...........ee.eeeee.hhhhhhhhhhhhhhhh...........ee...hhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh.eeeeee................eeee......ee...eeee.hhhh.eeeee....----......eeee..hhhhhhhhhhhhhhh........--------...........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o8r B  11 RDmSWLSFNERVLmEAADRTLPVYDRIKFLSIFSSNLEEFYTVRVAY------------------------LQAIRETVIRQDELYYRIFYDQILPTLEEHGIRLRTHAPTHPDHKAYLRRFFHEEIFPLLYPmLLLPSKVRTFIRSGRVYLAVRLKEKETDEAYSYALLNVPTDGLPRFVELPRLQTDTFYYYSFLEDIIKEHLDVVFPGYEVmDSYSIKVSR-----------------------------PTRFmYDGRmPDEVLRYI----------AIRSGNYVNLQDLAmLPNPFAPRLETLTPEPLLSKHLEQAPSLmEGIRRKDYLIHVPYYTYDYVVRLLmEAAISPDVSEIRLTQYRVAENSSIISALEAAAQSGKKVSVFVELKARFDEENNLRLSERmRRSGIRIVYSmPGLKVHAKTALILYHTPAGERPQGIALLSTGNFNETTARIYSDTTLmTANTDIVHDVYRLFRILDGDPEPARFSRLLVARYNmGEAITNLIEREIENVKRGKRGYmLLKmNGLQDKNVITQLYRASEAGVEIDLIVRGICCLVPDmPQSRNIRVTRLVDmYLEHSRIWCFHNGGKEEVFISSADW----LYNRIETACPVLDPTLRREIIDILEIQLRDNIKAC--------IYKHNSDEKPVRAQAAIYRYLKGKEET 690
                              |     20   |    30        40        50      |  -         -         - |      90       100       110       120       130       140   |   150       160       170       180       190       200       210       220    |  230   |     -         -         -   |   270  |    280|        - |     300     | 310       320       330    |  340       350       360       370       380       390       400       410       420       430|      440       450       460       470       480       490       500       510   |   520       530      |540|      550       560       570      |580       590|      600       610     |   -|      630       640       650    |    -   |   670       680       690
                             13-MSE     24-MSE                           57                       82                                                           144-MSE                                                                          225-MSE  234                           264   |    |     281        292           306-MSE                      335-MSE                  360-MSE                                                     420-MSE    431-MSE                                        478-MSE                             514-MSE                537-MSE                                 577-MSE       591-MSE                  616  621                               655      664                          
                                                                                                                                                                                                                                                                                           268-MSE|                                                                                                                                                                                                                                                                         541-MSE                                                                                                                                                 
                                                                                                                                                                                                                                                                                                273-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 8)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: PLD (22)
(-)
Clan: no clan defined [family: PP_kinase] (3)
(-)
Clan: no clan defined [family: PP_kinase_N] (3)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7MTR1_PORGI | Q7MTR1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008976    polyphosphate kinase activity    Catalysis of the reaction: ATP + phosphate(n) = ADP + phosphate(n+1).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006799    polyphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a polyphosphate, the anion or salt of polyphosphoric acid.
cellular component
    GO:0009358    polyphosphate kinase complex    A protein complex that possesses polyphosphate kinase activity.

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  2o8r
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 Related Entries

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