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(-) Description

Title :  CRYSTAL STRUCTURE OF INORGANIC POLYPHOSPHATE/ATP-NAD KINASE FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  S. Mori, M. Yamasaki, Y. Maruyama, K. Momma, S. Kawai, W. Hashimoto, B. Mikami, K. Murata
Date :  24 Nov 04  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Nad Kinase, Polyphosphate, Nad, Atp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mori, M. Yamasaki, Y. Maruyama, K. Momma, S. Kawai, W. Hashimoto, B. Mikami, K. Murata
Nad-Binding Mode And The Significance Of Intersubunit Contact Revealed By The Crystal Structure Of Mycobacterium Tuberculosis Nad Kinase-Nad Complex
Biochem. Biophys. Res. Commun. V. 327 500 2005
PubMed-ID: 15629142  |  Reference-DOI: 10.1016/J.BBRC.2004.11.163
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INORGANIC POLYPHOSPHATE/ATP-NAD KINASE
    Chains: A, B
    EC Number: 2.7.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSK27
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PPNK
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: POLY(P)/ATP NAD KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1Y3H)

(-) Sites  (0, 0)

(no "Site" information available for 1Y3H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y3H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y3H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y3H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y3H)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y3H)

(-) Sequences/Alignments

Asymmetric 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:268
 aligned with NADK_MYCTO | P9WHV6 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:303
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   
           NADK_MYCTO     5 RSVLLVVHTGRDEATETARRVEKVLGDNKIALRVLSAEAVDRGSLHLAPDDMRAMGVEIEVVDADQHAADGCELVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPMVTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRLPVTGWRGK 307
               SCOP domains d1y3ha_ A     : Inorganic polyphosph                              ate/ATP-NAD kinase PpnK                                                                                                                                                                                                                       SCOP domains
               CATH domains 1y3hA01 A     :5-139,A:277-307 Proba                              ble inorganic polyphosphate/atp-NAD kinase; domain 1                 1y3hA02 A:140-276 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                              1y3hA01 A:5-139,A:277-307       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..-----..hhhhhhhhhhh....eeee.------------------------------........eeeeehhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhh..eeeee..eeeeeee..eeeeeeee..eeeeee......eeeeeee..eeeeeeee.eeeee.hhhh.hhhhhhh..ee......eeeeee.........eee.....eeeee......eeeee...eeeee....eeeeee....eeeee....hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y3h A   5 RSVLLVVHT-----TETARRVEKVLGDNKIALRVLS------------------------------HAADGCELVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPMVTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRLPVIGWRGK 307
                                    |-    |   24        34     |   -         -         -      | 74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   
                                   13    19                   40                             71                                                                                                                                                                                                                                            


Chain A from PDB  Type:PROTEIN  Length:268
 aligned with NADK_MYCTU | P9WHV7 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:303
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   
           NADK_MYCTU     5 RSVLLVVHTGRDEATETARRVEKVLGDNKIALRVLSAEAVDRGSLHLAPDDMRAMGVEIEVVDADQHAADGCELVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPMVTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRLPVTGWRGK 307
               SCOP domains d1y3ha_ A     : Inorganic polyphosph                              ate/ATP-NAD kinase PpnK                                                                                                                                                                                                                       SCOP domains
               CATH domains 1y3hA01 A     :5-139,A:277-307 Proba                              ble inorganic polyphosphate/atp-NAD kinase; domain 1                 1y3hA02 A:140-276 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                              1y3hA01 A:5-139,A:277-307       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..-----..hhhhhhhhhhh....eeee.------------------------------........eeeeehhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhh..eeeee..eeeeeee..eeeeeeee..eeeeee......eeeeeee..eeeeeeee.eeeee.hhhh.hhhhhhh..ee......eeeeee.........eee.....eeeee......eeeee...eeeee....eeeeee....eeeee....hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y3h A   5 RSVLLVVHT-----TETARRVEKVLGDNKIALRVLS------------------------------HAADGCELVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPMVTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRLPVIGWRGK 307
                                    |-    |   24        34     |   -         -         -      | 74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   
                                   13    19                   40                             71                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:267
 aligned with NADK_MYCTO | P9WHV6 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:303
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   
           NADK_MYCTO     5 RSVLLVVHTGRDEATETARRVEKVLGDNKIALRVLSAEAVDRGSLHLAPDDMRAMGVEIEVVDADQHAADGCELVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPMVTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRLPVTGWRGK 307
               SCOP domains d1y3hb_ B      : Inorganic polyphosp                              hate/ATP-NAD kinase PpnK                                                                                                                                                                                                                      SCOP domains
               CATH domains 1y3hB01 B      :5-139,B:277-307 Prob                              able inorganic polyphosphate/atp-NAD kinase; domain 1                1y3hB02 B:140-276 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                              1y3hB01 B:5-139,B:277-307       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..------.hhhhhhhhhhhh..eeeee.------------------------------........eeeeehhhhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeee...eeeee......eeeeeee..eeeeeeee.eeeee..hhhhhhhhhh...ee......eeeeee.........eee.....eeeee......eeeee...eeeee....eeeeeeeeeeeeeee....hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y3h B   5 RSVLLVVHT------ETARRVEKVLGDNKIALRVLS------------------------------HAADGCELVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPMVTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRLPVIGWRGK 307
                                    |-     |  24        34     |   -         -         -      | 74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   
                                   13     20                  40                             71                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:267
 aligned with NADK_MYCTU | P9WHV7 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:303
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   
           NADK_MYCTU     5 RSVLLVVHTGRDEATETARRVEKVLGDNKIALRVLSAEAVDRGSLHLAPDDMRAMGVEIEVVDADQHAADGCELVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPMVTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRLPVTGWRGK 307
               SCOP domains d1y3hb_ B      : Inorganic polyphosp                              hate/ATP-NAD kinase PpnK                                                                                                                                                                                                                      SCOP domains
               CATH domains 1y3hB01 B      :5-139,B:277-307 Prob                              able inorganic polyphosphate/atp-NAD kinase; domain 1                1y3hB02 B:140-276 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                              1y3hB01 B:5-139,B:277-307       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..------.hhhhhhhhhhhh..eeeee.------------------------------........eeeeehhhhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeee...eeeee......eeeeeee..eeeeeeee.eeeee..hhhhhhhhhh...ee......eeeeee.........eee.....eeeee......eeeee...eeeee....eeeeeeeeeeeeeee....hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y3h B   5 RSVLLVVHT------ETARRVEKVLGDNKIALRVLS------------------------------HAADGCELVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPMVTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRLPVIGWRGK 307
                                    |-     |  24        34     |   -         -         -      | 74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304   
                                   13     20                  40                             71
   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  (1, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Y3H)

(-) Gene Ontology  (14, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NADK_MYCTO | P9WHV6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003951    NAD+ kinase activity    Catalysis of the reaction: ATP + NAD(+) = ADP + 2 H(+) + NADP(+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0019674    NAD metabolic process    The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
    GO:0006741    NADP biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; biosynthesis may be of either the oxidized form, NADP, or the reduced form, NADPH.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B   (NADK_MYCTU | P9WHV7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0003951    NAD+ kinase activity    Catalysis of the reaction: ATP + NAD(+) = ADP + 2 H(+) + NADP(+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0019674    NAD metabolic process    The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
    GO:0006741    NADP biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; biosynthesis may be of either the oxidized form, NADP, or the reduced form, NADPH.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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:0006797    polyphosphate metabolic process    The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1y3h
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  NADK_MYCTO | P9WHV6
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  2.7.1.23
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NADK_MYCTO | P9WHV6: 1u0r 1u0t 1y3i
        NADK_MYCTU | P9WHV7: 1u0r 1u0t 1y3i

(-) Related Entries Specified in the PDB File

1y3i THE SAME PROTEIN, NAD COMPLEX