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(-) Description

Title :  CRYSTAL STRUCTURE OF A NAD KINASE FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH NAD
 
Authors :  J. Liu, Y. Lou, H. Yokota, P. D. Adams, R. Kim, S. H. Kim, Berkeley Structural Genomics Center (Bsgc)
Date :  02 Mar 05  (Deposition) - 26 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nad Kinase, Nad, Atp, Nadp, Structural Genomics, Psi, Protein Structure Initiative, Berkeley Structural Genomics Center, Bsgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Liu, Y. Lou, H. Yokota, P. D. Adams, R. Kim, S. H. Kim
Crystal Structures Of An Nad Kinase From Archaeoglobus Fulgidus In Complex With Atp, Nad, Or Nadp
J. Mol. Biol. V. 354 289 2005
PubMed-ID: 16242716  |  Reference-DOI: 10.1016/J.JMB.2005.09.026
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE
    Chains: A, B, C, D
    EC Number: 2.7.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PPNK
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: POLYP, /ATP NAD KINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:75 , ASN A:115 , GLU A:116 , ILE A:153 , THR A:156 , TYR A:158 , SER A:161 , ASP A:209 , GLY A:210 , ALA D:125 , LYS D:126 , MET D:127 , ARG D:143 , ASP D:145 , ALA D:180 , PHE D:182BINDING SITE FOR RESIDUE NAD A 3075
2AC2SOFTWAREASP B:49 , LEU B:53 , ARG B:54 , ASN B:115 , GLU B:116 , ILE B:153 , THR B:156 , GLY B:157 , TYR B:158 , SER B:161 , ASP B:209 , GLY B:210 , GLN B:211 , ALA C:125 , LYS C:126 , MET C:127 , ARG C:143 , ASP C:145 , ALA C:180 , PHE C:182BINDING SITE FOR RESIDUE NAD B 3076
3AC3SOFTWAREALA B:125 , LYS B:126 , MET B:127 , ARG B:143 , ASP B:145 , ALA B:180 , PHE B:182 , ASP C:49 , ARG C:54 , ARG C:72 , LEU C:75 , ASN C:115 , GLU C:116 , ILE C:153 , THR C:156 , TYR C:158 , SER C:161 , ASP C:209 , GLY C:210 , GLN C:211BINDING SITE FOR RESIDUE NAD C 3077
4AC4SOFTWAREALA A:125 , LYS A:126 , MET A:127 , ARG A:143 , ASP A:145 , ALA A:180 , PHE A:182 , HOH A:3076 , ASP D:49 , LEU D:75 , ASN D:115 , GLU D:116 , ILE D:153 , THR D:156 , TYR D:158 , SER D:161 , ASP D:209 , GLY D:210 , GLN D:211BINDING SITE FOR RESIDUE NAD D 3078

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z0Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z0Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z0Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z0Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z0Z)

(-) 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:249
 aligned with NADK_ARCFU | O30297 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           NADK_ARCFU     1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
               SCOP domains d1z0za_ A: Inorganic polyphosphate/ATP-NAD kinase PpnK                                                                                                                                                                                                    SCOP domains
               CATH domains 1z0zA01 A:1-101,A:227-249 Probable inorganic polyphosphate/atp-NAD kinase; domain 1                  1z0zA02 A:102-226 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                  1z0zA01                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh..eeeee...hhhhhhh.eeeeeehhhhhhhhhh.......eeeee.............hhhhhhhhhhhhh...ee..eee......ee..eeeeee......eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh...ee.....eeeeeee.........eeee....eeee...eeeee...eeeee..eeeeee....ee.....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0z A   1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with NADK_ARCFU | O30297 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           NADK_ARCFU     1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
               SCOP domains d1z0zb_ B: Inorganic polyphosphate/ATP-NAD kinase PpnK                                                                                                                                                                                                    SCOP domains
               CATH domains 1z0zB01 B:1-101,B:227-249 Probable inorganic polyphosphate/atp-NAD kinase; domain 1                  1z0zB02 B:102-226 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                  1z0zB01                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh..eeeee...hhhhhhh.eeeeeehhhhhhhhhhh......eeeee.............hhhhhhhhhhhhh.eeee..eee..........eeeeee......eeeeeee..eeeeeeee.eeeeee.hhhhhhhhhh...ee......eeeeee.........eee.....eeeeeeeeeeee...eeeeeeeeeeeee....eeee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0z B   1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         


Chain C from PDB  Type:PROTEIN  Length:249
 aligned with NADK_ARCFU | O30297 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           NADK_ARCFU     1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
               SCOP domains d1z0zc_ C: Inorganic polyphosphate/ATP-NAD kinase PpnK                                                                                                                                                                                                    SCOP domains
               CATH domains 1z0zC01 C:1-101,C:227-249 Probable inorganic polyphosphate/atp-NAD kinase; domain 1                  1z0zC02 C:102-226 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                  1z0zC01                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhh...eeeee...hhhhhhh.eeeee.hhhhhhhhhh.......eeee..............hhhhhhhhhhhhh.eeee..ee.......ee..eeeeee......eeeeeee..eeeeeeee.eeeeee.hhhhhhhhhh...ee......eeeee..........eee.....eeeeeeeeeeee...eeeeeeeeeeeee....eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0z C   1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         


Chain D from PDB  Type:PROTEIN  Length:249
 aligned with NADK_ARCFU | O30297 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           NADK_ARCFU     1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
               SCOP domains d1z0zd_ D: Inorganic polyphosphate/ATP-NAD kinase PpnK                                                                                                                                                                                                    SCOP domains
               CATH domains 1z0zD01 D:1-101,D:227-249 Probable inorganic polyphosphate/atp-NAD kinase; domain 1                  1z0zD02 D:102-226 Probable inorganic polyphosphate/atp-NAD kinase; domain 2                                                  1z0zD01                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh..eeeee...hhhhhh..eeeeeehhhhhhhhhhh.........ee.............hhhhhhhhhhhhh.eeee..eee..........eeeeee......eeeeeee...eeeeeee.eeeeee.hhhhhhhhhhh..ee......eeeeee.........eee.....eeeeeeeeeeee...eeeeeeeeeeeee....eeee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z0z D   1 MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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, 4)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Z0Z)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (NADK_ARCFU | O30297)
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NADK_ARCFU | O30297: 1suw 1z0s 1z0u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Z0Z)