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(-) Description

Title :  CRYSTAL STRUCTURE OF BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE KINASE/3,6-DICHLOROBENZO[B]THIOPHENE-2-CARBOXYLIC ACID COMPLEX WITH ADP
 
Authors :  S. C. Tso, J. L. Chuang, W. J. Gui, R. M. Wynn, J. Li, D. T. Chuang
Date :  01 Mar 12  (Deposition) - 27 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
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
Crystal Structure Of Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase/3, 6-Dichlorobenzo[B]Thiophene-2-Carboxylic Acid Complex With Adp
To Be Published
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: 511693
    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
10F11Ligand/Ion3,6-DICHLORO-1-BENZOTHIOPHENE-2-CARBOXYLIC ACID
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3K1Ligand/IonPOTASSIUM ION
4MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
10F12Ligand/Ion3,6-DICHLORO-1-BENZOTHIOPHENE-2-CARBOXYLIC ACID
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
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 , THR A:304 , THR A:305 , GLY A:335 , GLY A:337 , GLY A:339 , LEU A:340 , PRO A:341 , THR A:364 , K A:403 , MG A:404 , HOH A:501 , HOH A:512 , HOH A:535 , HOH A:565 , HOH A:566 , HOH A:568BINDING SITE FOR RESIDUE ADP A 401
2AC2SOFTWARELEU A:68 , ILE A:72 , TYR A:99 , HIS A:132 , ARG A:167 , ILE A:170 , ARG A:171BINDING SITE FOR RESIDUE 0F1 A 402
3AC3SOFTWAREVAL A:298 , ASP A:300 , PHE A:303 , GLY A:337 , PRO A:341 , ADP A:401BINDING SITE FOR RESIDUE K A 403
4AC4SOFTWAREASN A:249 , ADP A:401 , HOH A:565 , HOH A:566 , HOH A:567BINDING SITE FOR RESIDUE MG A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E00)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E00)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E00)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E00)

(-) Exons   (0, 0)

(no "Exon" information available for 4E00)

(-) 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:308
 aligned with BCKD_RAT | Q00972 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:336
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398      
             BCKD_RAT    69 RLTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFGFGLPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHID 404
               SCOP domains d4e00a1 A:39-185 automated matches                                                                                                                 d4e00a2 A:186-374 automated matches                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee..eeeeehhhhhhhhhhhhhhhhhhhhhh....eeeee.....eee.hhhhhhhhhhhhhhhhhhhhhh..........eeeeeee...eeeeeeee.....hhhhhh..........----------------------------...hhhhhhhhhhhhh..eeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4e00 A  39 RLTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTA----------------------------GFGFGLPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHID 374
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       | -         -         -      |338       348       358       368      
                                                                                                                                                                                                                                                                                                     306                          335
   Legend:   → Mismatch (orange background)
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  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 4E00)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E00)

(-) 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 3tz5 3vad 4dzy 4e01 4e02 4h7q 4h81 4h85

(-) Related Entries Specified in the PDB File

3tz0 THE SAME PROTEIN WITH DIFFERENT INHIBITOR
3tz2 THE SAME PROTEIN WITH DIFFERENT INHIBITOR
3tz4 THE SAME PROTEIN WITH DIFFERENT INHIBITOR
3tz5 THE SAME PROTEIN WITH DIFFERENT INHIBITOR
4dzy THE SAME PROTEIN WITH DIFFERENT INHIBITOR
4e01