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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOSIDE-DIPHOSPHATE KINASE FROM BORRELIA BURGDORFERI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  30 Jan 12  (Deposition) - 08 Feb 12  (Release) - 08 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Ssgcid, Nucleoside Diphosphate Kinase, Kinase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Niaid, National Institute Of Allergy And Infectious Diseases, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid), D. R. Davies, J. A. Abendroth, D. Fox Iii, B. Staker, L. Stewart
Crystal Structure Of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
    Chains: A, B, C, D, E, F
    EC Number: 2.7.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: NUCLEOSIDE-DIPHOSPHATE KINASE
    Gene: NDK, BB_0463
    Organism Common: LYME DISEASE SPIROCHETE
    Organism Scientific: BORRELIA BURGDORFERI
    Organism Taxid: 139
    Synonym: NDK, 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4DI6)

(-) Sites  (0, 0)

(no "Site" information available for 4DI6)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:164 -A:169
2B:164 -B:169
3C:164 -C:169
4D:164 -D:169
5E:164 -E:169
6F:164 -F:169

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DI6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DI6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DI6)

(-) Exons   (0, 0)

(no "Exon" information available for 4DI6)

(-) 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:169
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:169
                              1                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158         
            NDK_BORBU     - --MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4di6a_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhh..........hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4di6 A   1 MSMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain B from PDB  Type:PROTEIN  Length:169
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:169
                              1                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158         
            NDK_BORBU     - --MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4di6b_ B: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhh..........hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4di6 B   1 MSMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain C from PDB  Type:PROTEIN  Length:166
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:166
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      
            NDK_BORBU     2 LLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4di6c_ C: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhh..........hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4di6 C   4 LLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163      


Chain D from PDB  Type:PROTEIN  Length:169
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:169
                              1                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158         
            NDK_BORBU     - --MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4di6d_ D: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhh..........hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4di6 D   1 MSMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain E from PDB  Type:PROTEIN  Length:168
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
            NDK_BORBU     - -MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4di6e_ E: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhh..........hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4di6 E   2 SMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        


Chain F from PDB  Type:PROTEIN  Length:168
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
            NDK_BORBU     - -MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4di6f_ F: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhh..........hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4di6 F   2 SMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DI6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DI6)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (NDK_BORBU | O51419)
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: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.
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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        NDK_BORBU | O51419: 4dz6

(-) Related Entries Specified in the PDB File

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