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(-) Description

Title :  2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP
 
Authors :  T. H. Tahirov, E. Inagaki
Date :  12 Apr 04  (Deposition) - 14 Apr 04  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  2-Keto-3-Deoxygluconate Kinase, Atp, Thermus Thermophilus, Structural Genomics, Transferase, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Ohshima, E. Inagaki, K. Yasuike, K. Takio, T. H. Tahirov
Structure Of Thermus Thermophilus 2-Keto-3-Deoxygluconate Kinase: Evidence For Recognition Of An Open Chain Substrate
J. Mol. Biol. V. 340 477 2004
PubMed-ID: 15210349  |  Reference-DOI: 10.1016/J.JMB.2004.04.074
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-KETO-3-DEOXYGLUCONATE KINASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    StrainHB8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2KDG2Ligand/Ion2-KETO-3-DEOXYGLUCONATE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1ADP6Ligand/IonADENOSINE-5'-DIPHOSPHATE
2KDG6Ligand/Ion2-KETO-3-DEOXYGLUCONATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:11 , GLY A:34 , ALA A:35 , ASN A:38 , TYR A:89 , TYR A:103 , ARG A:105 , ILE A:134 , ARG A:167 , GLY A:248 , ASP A:251 , ASP A:287 , HOH A:2050 , HOH A:2117BINDING SITE FOR RESIDUE KDG A1302
2AC2SOFTWARELYS A:219 , GLY A:221 , GLY A:224 , PHE A:239 , ALA A:249 , GLY A:250 , ASN A:275 , ALA A:279 , HOH A:2073 , HOH A:2074 , HOH A:2117 , HOH A:2118 , HOH A:2119 , HOH A:2120BINDING SITE FOR RESIDUE ADP A1303
3AC3SOFTWAREGLY B:34 , ALA B:35 , ASN B:38 , TYR B:89 , TYR B:103 , ARG B:105 , ILE B:134 , ARG B:167 , ASP B:251 , ASP B:287 , HOH B:2040BINDING SITE FOR RESIDUE KDG B1302
4AC4SOFTWARELYS B:219 , GLY B:221 , GLY B:224 , PHE B:239 , ALA B:243 , GLY B:250 , PHE B:253 , ASN B:275 , HOH B:2058 , HOH B:2089 , HOH B:2091BINDING SITE FOR RESIDUE ADP B1303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V1A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V1A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V1A)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.KDGK_THET8245-258
 
  2A:245-258
B:245-258
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.KDGK_THET8245-258
 
  6A:245-258
B:245-258

(-) Exons   (0, 0)

(no "Exon" information available for 1V1A)

(-) 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:302
 aligned with KDGK_THET8 | Q53W83 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:302
                                    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       260       270       280       290       300  
           KDGK_THET8     1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLLK 302
               SCOP domains d1v1aa_ A: 2-keto-3-deoxygluconate kinase                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1v1aA00 A:1-302  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeee.....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh.....eee......eeeeee.....eeeeee....hhhhh.....hhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2-------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v1a A   1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLLK 302
                                    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       260       270       280       290       300  

Chain B from PDB  Type:PROTEIN  Length:302
 aligned with KDGK_THET8 | Q53W83 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:302
                                    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       260       270       280       290       300  
           KDGK_THET8     1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLLK 302
               SCOP domains d1v1ab_ B: 2-keto-3-deoxygluconate kinase                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1v1aB00 B:1-302  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh......eee......eeeeee.....eeeeee...hhhhh......hhhhh.......ee.hhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhhhhhh.eeeeehhhhhhh..hhhhhhhhh...eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2-------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v1a B   1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLLK 302
                                    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       260       270       280       290       300  

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V1A)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KDGK_THET8 | Q53W83)
molecular function
    GO:0008673    2-dehydro-3-deoxygluconokinase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + 2 H(+).
    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: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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    GO:0004747    ribokinase activity    Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate.
    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:0006014    D-ribose metabolic process    The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0046835    carbohydrate phosphorylation    The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KDGK_THET8 | Q53W831v19 1v1b 1v1s

(-) Related Entries Specified in the PDB File

1j5v CRYSTAL STRUCTURE OF 2-KETO-3-DEOXYGLUCONATE KINASE (TM0067)FROM THERMOTOGA MARITIMA AT 2.3 A RESOLUTION
1v19 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS
1v1b 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND ATP