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(-) Description

Title :  CRYSTAL STRUCTURE OF NAD KINASE FROM THERMOTOGA MARITIMA
 
Authors :  Berkeley Structural Genomics Center (Bsgc)
Date :  09 Feb 05  (Deposition) - 05 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 5:  A (1x),B (1x)
Biol. Unit 6:  C (1x),D (1x)
Biol. Unit 7:  A (1x),B (1x)
Biol. Unit 8:  C (1x),D (1x)
Keywords :  Domain 1: Alpha/Beta Domain2: Beta Sandwich, Structural Genomics, Psi, Protein Structure Initiative, Berkeley Structural Genomics Center, Bsgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Oganesyan, C. Huang, P. D. Adams, J. Jancarik, H. A. Yokota, R. Kim, S. H. Kim
Structure Of A Nad Kinase From Thermotoga Maritima At 2. 3 A Resolution.
Acta Crystallogr. , Sect. F V. 61 640 2005
PubMed-ID: 16511117  |  Reference-DOI: 10.1107/S1744309105019780
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INORGANIC POLYPHOSPHATE/ATP-NAD KINASE
    Chains: A, B, C, D
    EC Number: 2.7.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI K12
    Expression System Plasmid: PB4.1316B
    Expression System Strain: K12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Fragment: NAD KINASE
    Gene: PPNK
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: POLY(P)/ATP NAD KINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 4 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 5 (1x): A (1x)B (1x)  
Biological Unit 6 (1x):   C (1x)D (1x)
Biological Unit 7 (1x): A (1x)B (1x)  
Biological Unit 8 (1x):   C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 18)

Asymmetric Unit (1, 18)
No.NameCountTypeFull Name
1SO418Ligand/IonSULFATE ION
Biological Unit 1 (1, 13)
No.NameCountTypeFull Name
1SO413Ligand/IonSULFATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 3 (1, 13)
No.NameCountTypeFull Name
1SO413Ligand/IonSULFATE ION
Biological Unit 4 (1, 13)
No.NameCountTypeFull Name
1SO413Ligand/IonSULFATE ION
Biological Unit 5 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 6 (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 7 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 8 (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:113 , ASN A:114 , SO4 A:309BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWARESO4 A:304 , SO4 A:309 , GLY B:113 , ASN B:114BINDING SITE FOR RESIDUE SO4 B 302
03AC3SOFTWAREGLY D:113 , ASN D:114BINDING SITE FOR RESIDUE SO4 D 303
04AC4SOFTWAREHIS A:115 , LEU A:116 , SO4 A:309 , SO4 B:302BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREGLY C:113 , ASN C:114 , SO4 D:308BINDING SITE FOR RESIDUE SO4 C 305
06AC6SOFTWAREGLY D:50 , ASP D:51 , LYS D:71 , LYS D:250BINDING SITE FOR RESIDUE SO4 D 306
07AC7SOFTWAREGLY C:50 , ASP C:51BINDING SITE FOR RESIDUE SO4 C 307
08AC8SOFTWAREASN C:114 , HIS C:115 , SO4 C:305 , ASN D:114 , HIS D:115 , SO4 D:314BINDING SITE FOR RESIDUE SO4 D 308
09AC9SOFTWAREASN A:114 , HIS A:115 , SO4 A:301 , SO4 A:304 , ASN B:114 , HIS B:115 , SO4 B:302BINDING SITE FOR RESIDUE SO4 A 309
10BC1SOFTWAREGLY B:50 , ASP B:51 , LYS B:71 , LYS B:250BINDING SITE FOR RESIDUE SO4 B 310
11BC2SOFTWAREASP D:126 , LEU D:127BINDING SITE FOR RESIDUE SO4 D 311
12BC3SOFTWAREARG D:207 , ASP D:208 , LYS D:222BINDING SITE FOR RESIDUE SO4 D 312
13BC4SOFTWAREARG A:248 , ARG A:255 , ARG A:256BINDING SITE FOR RESIDUE SO4 A 313
14BC5SOFTWAREHIS D:115 , LEU D:116 , SO4 D:308BINDING SITE FOR RESIDUE SO4 D 314
15BC6SOFTWAREARG D:248 , ASP D:249 , ARG D:255 , ARG D:256BINDING SITE FOR RESIDUE SO4 D 315
16BC7SOFTWAREARG A:207 , ASP A:208 , LYS A:222BINDING SITE FOR RESIDUE SO4 A 316
17BC8SOFTWAREGLY A:50 , ASP A:51 , GLY A:52 , ARG A:74 , LEU A:75 , GLY A:76 , LYS A:250BINDING SITE FOR RESIDUE SO4 A 317
18BC9SOFTWAREARG B:248 , ARG B:255 , ARG B:256BINDING SITE FOR RESIDUE SO4 B 318

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YT5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YT5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YT5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YT5)

(-) Exons   (0, 0)

(no "Exon" information available for 1YT5)

(-) 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:256
 aligned with NADK_THEMA | Q9X255 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      
           NADK_THEMA     1 MKIAILYREEREKEGEFLKEKISKEHEVIEFGEANAPGRVTADLIVVVGGDGTVLKAAKKAADGTPMVGFKAGRLGFLTSYTLDEIDRFLEDLRNWNFREETRWFIQIESELGNHLALNDVTLERDLSGKMVEIEVEVEHHSSMWFFADGVVISTPTGSTAYSLSIGGPIIFPECEVLEISPIAPQFFLTRSVVIPSNFKVVVESQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPEYDYVTVIRDKLGYGRR 256
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh...eeeeeee..........eeeeeehhhhhhhhhh......eeeeee..........hhhhhhhhhhhhhh...eeeeeeeeeeee..eeeee..eeeee.......eeeeeee.....eeeee.eeeee.hhhhhh...............eeeeeee.........eeee....eeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeee....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yt5 A   1 MKIAILYREEREKEGEFLKEKISKEHEVIEFGEANAPGRVTADLIVVVGGDGTVLKAAKKAADGTPMVGFKAGRLGFLTSYTLDEIDRFLEDLRNWNFREETRWFIQIESELGNHLALNDVTLERDLSGKMVEIEVEVEHHSSMWFFADGVVISTPTGSTAYSLSIGGPIIFPECEVLEISPIAPQFFLTRSVVIPSNFKVVVESQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPEYDYVTVIRDKLGYGRR 256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with NADK_THEMA | Q9X255 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      
           NADK_THEMA     1 MKIAILYREEREKEGEFLKEKISKEHEVIEFGEANAPGRVTADLIVVVGGDGTVLKAAKKAADGTPMVGFKAGRLGFLTSYTLDEIDRFLEDLRNWNFREETRWFIQIESELGNHLALNDVTLERDLSGKMVEIEVEVEHHSSMWFFADGVVISTPTGSTAYSLSIGGPIIFPECEVLEISPIAPQFFLTRSVVIPSNFKVVVESQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPEYDYVTVIRDKLGYGRR 256
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh..eeeeeee..........eeeee.hhhhhhhhhhhh....eeeeee.........ee..hhhhhhhhhhh...eeeeeeeeeeee..eeeee..eeeee.......eeeeeee.....eeeee.eeeee.hhhhhh.hhhhh.........eeeeeee.........eeee....eeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeee....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yt5 B   1 MKIAILYREEREKEGEFLKEKISKEHEVIEFGEANAPGRVTADLIVVVGGDGTVLKAAKKAADGTPMVGFKAGRLGFLTSYTLDEIDRFLEDLRNWNFREETRWFIQIESELGNHLALNDVTLERDLSGKMVEIEVEVEHHSSMWFFADGVVISTPTGSTAYSLSIGGPIIFPECEVLEISPIAPQFFLTRSVVIPSNFKVVVESQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPEYDYVTVIRDKLGYGRR 256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      


Chain C from PDB  Type:PROTEIN  Length:252
 aligned with NADK_THEMA | Q9X255 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      
           NADK_THEMA     1 MKIAILYREEREKEGEFLKEKISKEHEVIEFGEANAPGRVTADLIVVVGGDGTVLKAAKKAADGTPMVGFKAGRLGFLTSYTLDEIDRFLEDLRNWNFREETRWFIQIESELGNHLALNDVTLERDLSGKMVEIEVEVEHHSSMWFFADGVVISTPTGSTAYSLSIGGPIIFPECEVLEISPIAPQFFLTRSVVIPSNFKVVVESQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPEYDYVTVIRDKLGYGRR 256
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh...eeeeeee..........eeeee.hhhhhhhhhh......eeeee----..........hhhhhhhhhhh...eeeeeeeeeeee..eeeee..eeeee.......eeeeeee.....eeeee.eeeee..hhhhhhhhhh..........eeeeeee.........eeee....eeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeee....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yt5 C   1 MKIAILYREEREKEGEFLKEKISKEHEVIEFGEANAPGRVTADLIVVVGGDGTVLKAAKKAADGTPMVGF----LGFLTSYTLDEIDRFLEDLRNWNFREETRWFIQIESELGNHLALNDVTLERDLSGKMVEIEVEVEHHSSMWFFADGVVISTPTGSTAYSLSIGGPIIFPECEVLEISPIAPQFFLTRSVVIPSNFKVVVESQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPEYDYVTVIRDKLGYGRR 256
                                    10        20        30        40        50        60        70    |   80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      
                                                                                                70   75                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:256
 aligned with NADK_THEMA | Q9X255 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      
           NADK_THEMA     1 MKIAILYREEREKEGEFLKEKISKEHEVIEFGEANAPGRVTADLIVVVGGDGTVLKAAKKAADGTPMVGFKAGRLGFLTSYTLDEIDRFLEDLRNWNFREETRWFIQIESELGNHLALNDVTLERDLSGKMVEIEVEVEHHSSMWFFADGVVISTPTGSTAYSLSIGGPIIFPECEVLEISPIAPQFFLTRSVVIPSNFKVVVESQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPEYDYVTVIRDKLGYGRR 256
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh..eeeeeee..........eeeeeehhhhhhhhhh......eeeeee.........ee..hhhhhhhhhhhh..eeeeeeeeeeee..eeeee..eeeee.......eeeeeee.....eeeee.eeeee..hhhhhhhhhh..........eeeeeee.........eeee....eeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeee....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yt5 D   1 MKIAILYREEREKEGEFLKEKISKEHEVIEFGEANAPGRVTADLIVVVGGDGTVLKAAKKAADGTPMVGFKAGRLGFLTSYTLDEIDRFLEDLRNWNFREETRWFIQIESELGNHLALNDVTLERDLSGKMVEIEVEVEHHSSMWFFADGVVISTPTGSTAYSLSIGGPIIFPECEVLEISPIAPQFFLTRSVVIPSNFKVVVESQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPEYDYVTVIRDKLGYGRR 256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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  (0, 0)

(no "SCOP Domain" information available for 1YT5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YT5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YT5)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (NADK_THEMA | Q9X255)
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.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1suw NAD KINASE FROM DIFFERENT ORGANISM RELATED ID: BSGCAIR30585 RELATED DB: TARGETDB
1u0r NAD KINASE FROM DIFFERENT ORGANISM
1u0t NAD KINASE FROM DIFFERENT ORGANISM