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(-) Description

Title :  CRYSTAL STRUCTURE OF BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE/PHENYLBUTYRATE COMPLEX WITH ADP
 
Authors :  S. C. Tso, J. L. Chuang, W. J. Gui, R. M. Wynn, J. Li, D. T. Chuang
Date :  27 Sep 11  (Deposition) - 03 Oct 12  (Release) - 29 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ghkl Protein Kinase, Allosteric Kinase Inhibitor, Branched-Chain Alpha-Ketoacid, Branched-Chain Amino Acids, Maple Syrup Urine Disease, Diabetes And Obesity, Bergerat Nucleotide-Binding Fold, Protein Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Tso, J. L. Chuang, W. J. Gui, R. M. Wynn, J. Li, D. T. Chuang
Structures Of Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase-Inhibitor Complexes
Proc. Natl. Acad. Sci. Usa 2013
PubMed: search

(-) Compounds

Molecule 1 - [3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE, MITOCHONDRIAL
    Chains: A
    EC Number: 2.7.11.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCKHISB
    Expression System Strain: BL21GROESL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BCKDK
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE, BCKD- KINASE, BCKDHKIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CLT1Ligand/Ion4-PHENYL-BUTANOIC ACID
3K1Ligand/IonPOTASSIUM ION
4MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CLT2Ligand/Ion4-PHENYL-BUTANOIC ACID
3K-1Ligand/IonPOTASSIUM ION
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:249 , ARG A:252 , ALA A:253 , ASP A:285 , GLY A:289 , ILE A:290 , VAL A:298 , PHE A:303 , THR A:304 , THR A:305 , HIS A:334 , GLY A:335 , PHE A:336 , GLY A:337 , GLY A:339 , LEU A:340 , PRO A:341 , THR A:364 , MG A:390 , K A:391 , HOH A:394 , HOH A:397 , HOH A:407 , HOH A:409 , HOH A:412 , HOH A:415BINDING SITE FOR RESIDUE ADP A 389
2AC2SOFTWAREASN A:249 , ADP A:389 , HOH A:397 , HOH A:411 , HOH A:412BINDING SITE FOR RESIDUE MG A 390
3AC3SOFTWAREVAL A:298 , ASP A:300 , PHE A:303 , GLY A:337 , ADP A:389BINDING SITE FOR RESIDUE K A 391
4AC4SOFTWARELEU A:68 , TYR A:99 , LEU A:128 , HIS A:132 , VAL A:135 , ARG A:167 , ILE A:170 , ARG A:171BINDING SITE FOR RESIDUE CLT A 392

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TZ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TZ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TZ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TZ5)

(-) Exons   (0, 0)

(no "Exon" information available for 3TZ5)

(-) 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:312
 aligned with BCKD_RAT | Q00972 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:339
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396         
             BCKD_RAT    67 SVRLTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFGFGLPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHIDG 405
               SCOP domains d3tz5a1 A:37-185 automated matches                                                                                                                   d3tz5a2 A:186-375 automated matches                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee..eeeeehhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeehhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee...eeeeeeee.....................---------------------------....hhhhhhhhhhhhh..eeeeeee...eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tz5 A  37 SVRLTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTA---------------------------HGFGFGLPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHIDG 375
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306         -         -       336       346       356       366         
                                                                                                                                                                                                                                                                                                       306                         334
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TZ5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TZ5)

(-) Gene Ontology  (14, 14)

Asymmetric 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3tz0 THE SAME PROTEIN WITH DIFFERENT INHIBITOR
3tz2 THE SAME PROTEIN AND INHIBITOR WITH/WITHOUT ADP
3tz4 THE SAME PROTEIN WITH DIFFERENT INHIBITOR
4dzy
4h7q
4h81
4h85