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(-) Description

Title :  BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE (BCK) COMPLXED WITH ADP
 
Authors :  M. Machius, J. L. Chuang, R. M. Wynn, D. R. Tomchick, D. T. Chuang
Date :  22 Aug 01  (Deposition) - 11 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Mitochondrial Protein Kinase, Potassium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Machius, J. L. Chuang, R. M. Wynn, D. R. Tomchick, D. T. Chuang
Structure Of Rat Bckd Kinase: Nucleotide-Induced Domain Communication In A Mitochondrial Protein Kinase.
Proc. Natl. Acad. Sci. Usa V. 98 11218 2001
PubMed-ID: 11562470  |  Reference-DOI: 10.1073/PNAS.201220098

(-) Compounds

Molecule 1 - [3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE
    Chains: A
    EC Number: 2.7.1.115
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCKINASEHIS6/PGROESL
    Expression System Strain: CG-712
    Expression System Taxid: 562
    Expression System Vector: PTRCHISB
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: C-TERMINAL HIS6-TAG
    Synonym: BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL3Ligand/IonCHLORIDE ION
3K1Ligand/IonPOTASSIUM ION
4MG1Ligand/IonMAGNESIUM ION
5XE2Ligand/IonXENON

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:249 , HIS A:334 , ADP A:601 , HOH A:2072 , HOH A:2100 , HOH A:2124BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREVAL A:298 , ASP A:300 , PHE A:303 , GLY A:337 , PRO A:341 , ADP A:601BINDING SITE FOR RESIDUE K A 402
3AC3SOFTWAREILE A:235BINDING SITE FOR RESIDUE CL A 701
4AC4SOFTWAREHOH A:2009BINDING SITE FOR RESIDUE CL A 702
5AC5SOFTWAREHIS A:132BINDING SITE FOR RESIDUE XE A 502
6AC6SOFTWAREASN A:249 , ARG A:252 , ALA A:253 , ASP A:285 , GLY A:289 , ILE A:290 , VAL A:298 , THR A:304 , THR A:305 , HIS A:334 , PHE A:336 , GLY A:337 , GLY A:339 , LEU A:340 , PRO A:341 , THR A:364 , MG A:401 , K A:402 , HOH A:2091 , HOH A:2100 , HOH A:2122 , HOH A:2123 , HOH A:2124 , HOH A:2125BINDING SITE FOR RESIDUE ADP A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GKZ)

(-) 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:316
 aligned with BCKD_RAT | Q00972 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:341
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407 
             BCKD_RAT    68 VRLTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFGFGLPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHIDGREE 408
               SCOP domains d1gkza1 A:38-185 Branched-chain alpha-ketoacid dehydrogenase kinase (BCK)                                                                           d1gkza2 A:186-378 Branched-chain alpha-ketoacid dehydrogenase kinase (BCK)                                                                                                                        SCOP domains
               CATH domains 1gkzA02 A:38-193  [code=1.20.140.20, no name defined]                                                                                                       1gkzA01 A:194-377  [code=3.30.565.10, no name defined]                                                                                                                                  - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......ee..eeeeehhhhhhhhhhhhhhhhhhhhhh....eeeee.....eee.hhhhhhhhhhhhhhhhhhhhhh..........eeeeeee...eeeeeee......................-------------------------......hhhhhhhhhhhhh..eeeeeee...eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gkz A  38 VRLTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTA-------------------------PMHGFGFGLPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHIDGREE 378
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297        |-         -         -    |  337       347       357       367       377 
                                                                                                                                                                                                                                                                                                      306                       332
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BCKD_RAT | Q00972)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0047323    [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity    Catalysis of the reaction: ATP + 3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring) = ADP + 3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring) phosphate.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine 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.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0009083    branched-chain amino acid catabolic process    The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0005947    mitochondrial alpha-ketoglutarate dehydrogenase complex    Mitochondrial complex that possesses alpha-ketoglutarate dehydrogenase activity.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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  2.7.1.115
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 Related Entries

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

UniProtKB/Swiss-Prot
        BCKD_RAT | Q00972: 1gjv 1gkx 3tz0 3tz2 3tz4 3tz5 3vad 4dzy 4e00 4e01 4e02 4h7q 4h81 4h85

(-) Related Entries Specified in the PDB File

1gjv BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE (BCK) COMPLXED WITH ATP-GAMMA-S
1gkx BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE (BCK)