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(-) Description

Title :  STRUCTURE OF A HALOPHILIC NUCLEOSIDE DIPHOSPHATE KINASE FROM HALOBACTERIUM SALINARUM
 
Authors :  H. Besir, K. Zeth, A. Bracher, U. Heider, M. Ishibashi, M. Tokunaga, D. Oesterhelt
Date :  09 Sep 05  (Deposition) - 20 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Halophilic, Surface Charges, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Besir, K. Zeth, A. Bracher, U. Heider, M. Ishibashi, M. Tokunaga, D. Oesterhelt
Structure Of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum
Febs Lett. V. 579 6595 2005
PubMed-ID: 16293253  |  Reference-DOI: 10.1016/J.FEBSLET.2005.10.052
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
    ChainsA, B, C, D, E, F
    EC Number2.7.4.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21[DE3]
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificHALOBACTERIUM SALINARUM
    Organism Taxid2242
    SynonymNDK, NDP KINASE, NUCLEOSIDE-2-P KINASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA C:134 , PHE C:137 , ASP C:138 , GLU D:47BINDING SITE FOR RESIDUE CA C 201
2AC2SOFTWAREGLU C:47 , ALA D:134 , PHE D:137 , ASP D:138 , HOH D:225BINDING SITE FOR RESIDUE CA D 202
3AC3SOFTWAREHIS A:52 , GLU A:55 , ARG A:131 , HOH A:222BINDING SITE FOR RESIDUE CA A 203
4AC4SOFTWAREASP C:138 , ASP D:45 , GLU D:47 , HOH D:213BINDING SITE FOR RESIDUE CA C 204
5AC5SOFTWAREASP C:45 , ASP D:138BINDING SITE FOR RESIDUE CA D 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AZ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AZ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AZ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AZ1)

(-) Exons   (0, 0)

(no "Exon" information available for 2AZ1)

(-) 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:155
 aligned with NDK_HALSA | P61136 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:155
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153     
            NDK_HALSA     4 HDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
               SCOP domains d2az1a1 A:4-158 Nucleoside diphosphate kinase, NDK                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee......hhhhhhhhhhhhhhhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2az1 A   4 HDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153     

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with NDK_HALSA | P61136 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      
            NDK_HALSA     3 DHDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
               SCOP domains d2az1b_ B: Nucleoside diphosphate kinase, NDK                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhh..-----hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee......hhhhhhhhhhh...........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2az1 B   3 DHDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAE-----FFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
                                    12        22        32        42        52  |     62        72        82        92       102       112       122       132       142       152      
                                                                               55    61                                                                                                 

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with NDK_HALSA | P61136 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:155
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153     
            NDK_HALSA     4 HDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
               SCOP domains d2az1c_ C: Nucleoside diphosphate kinase, NDK                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee......hhhhhhhhhhh...........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2az1 C   4 HDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153     

Chain D from PDB  Type:PROTEIN  Length:155
 aligned with NDK_HALSA | P61136 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:155
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153     
            NDK_HALSA     4 HDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
               SCOP domains d2az1d_ D: Nucleoside diphosphate kinase, NDK                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee......hhhhhhhhhhhhhhhh......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2az1 D   4 HDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153     

Chain E from PDB  Type:PROTEIN  Length:154
 aligned with NDK_HALSA | P61136 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:154
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154    
            NDK_HALSA     5 DERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
               SCOP domains d2az1e_ E: Nucleoside diphosphate kinase, NDK                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee......hhhhhhhhhhhhhhhh......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2az1 E   5 DERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154    

Chain F from PDB  Type:PROTEIN  Length:151
 aligned with NDK_HALSA | P61136 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      
            NDK_HALSA     3 DHDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
               SCOP domains d2az1f_ F: Nucleoside diphosphate kinase, NDK                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhh...-----hhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee......hhhhhhhhhhhhhhhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2az1 F   3 DHDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEH-----FDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLA 158
                                    12        22        32        42        52   |    62        72        82        92       102       112       122       132       142       152      
                                                                                56    62                                                                                                

   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, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AZ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AZ1)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (NDK_HALSA | P61136)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004550    nucleoside diphosphate kinase activity    Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
    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:0006241    CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
    GO:0006183    GTP biosynthetic process    The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
    GO:0006228    UTP biosynthetic process    The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
    GO:0006165    nucleoside diphosphate phosphorylation    The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
    GO:0009142    nucleoside triphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    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:0006163    purine nucleotide metabolic process    The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NDK_HALSA | P611362az3

(-) Related Entries Specified in the PDB File

1nue GDP COMPLEX OF HUMAN NDK-B
2az3 THE SAME PROTEIN IN COMPLEX WITH CDP