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(-) Description

Title :  PYRUVATE DEHYDROGENASE KINASE, ISOZYME 2, CONTAINING ADP
 
Authors :  C. N. Steussy, K. M. Popov, M. M. Bowker-Kinley, R. B. Sloan, R. A. Harris, J. A. Hamilton
Date :  17 Jul 01  (Deposition) - 24 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Mitochondion, Serine Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. N. Steussy, K. M. Popov, M. M. Bowker-Kinley, R. B. Sloan Jr. , R. A. Harris, J. A. Hamilton
Structure Of Pyruvate Dehydrogenase Kinase. Novel Folding Pattern For A Serine Protein Kinase.
J. Biol. Chem. V. 276 37443 2001
PubMed-ID: 11483605  |  Reference-DOI: 10.1074/JBC.M104285200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVATE DEHYDROGENASE KINASE, ISOZYME 2
    ChainsA, B
    EC Number2.7.1.99
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A (NOVAGEN)
    Expression System StrainBL21[DE3]
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    Synonym[PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 2, MITOCHONDRIAL, PDK P45

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:1247 , ADP A:3500 , HOH A:4602 , HOH A:4603BINDING SITE FOR RESIDUE MG A 4601
2AC2SOFTWAREASN B:1247 , ADP B:3510 , HOH B:6003 , HOH B:6004BINDING SITE FOR RESIDUE MG B 4611
3AC3SOFTWAREASN A:1247 , ARG A:1250 , ALA A:1251 , ASP A:1282 , VAL A:1287 , LEU A:1295 , SER A:1301 , THR A:1302 , GLY A:1317 , PHE A:1318 , GLY A:1319 , GLY A:1321 , LEU A:1322 , THR A:1346 , MG A:4601 , HOH A:4603 , HOH A:6050 , HOH A:6098BINDING SITE FOR RESIDUE ADP A 3500
4AC4SOFTWAREASN B:1247 , ARG B:1250 , ALA B:1251 , ASP B:1282 , VAL B:1287 , LEU B:1295 , SER B:1301 , THR B:1302 , ALA B:1316 , GLY B:1317 , PHE B:1318 , GLY B:1319 , GLY B:1321 , LEU B:1322 , THR B:1346 , MG B:4611 , HOH B:6004 , HOH B:6006 , HOH B:6060BINDING SITE FOR RESIDUE ADP B 3510

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JM6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JM6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JM6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JM6)

(-) Exons   (0, 0)

(no "Exon" information available for 1JM6)

(-) 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:339
 aligned with PDK2_RAT | Q64536 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:364
                                    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       310       320       330       340       350       360       370    
            PDK2_RAT     11 ASLAGAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNCSVSDVVKDAYDMAKLLCDKYYMASPDLEIQEVNATNATQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLTLPPIKIMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVY  374
               SCOP domains d1jm6a1 A:1003-1169 Pyruvate d   ehydrogenase kinase                                                                                                                          d1jm6a2 A:1177-1366 Pyruvate dehydrogenase kinase                                                                                                                                              SCOP domains
               CATH domains 1jm6A02 A:1003-1180  [code=1.2   0.140.20, no name defined]                                                                                                                       1jm6A01 A:1181-1362  [code=3.30.565.10, no name defined]                                                                                                                              ---- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.......hhhhhhh..---.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.------......hhhhhhhhhhhhhhhhhhhhhhhhhhhh-------.......eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeeee.....hhhhhhhhhh.........---------....hhhhhhhhhhhhh..eeeeeee...eeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jm6 A 1003 ASLAGAPKYIEHFSKFSPSPLSMKQFLDFG---ACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEY------DPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFD-------PKHIGSIDPNCSVSDVVKDAYDMAKLLCDKYYMASPDLEIQEVNATNATQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLTLPPIKIMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTP---------AGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVY 1366
                                  1012      1022      1032   |  1042      1052      1062      1072      1082      1092      1102      1112      1122      |  -   |  1142      1152      1162      |  -    | 1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302   |     -   |  1322      1332      1342      1352      1362    
                                                      1032   |                                                                                         1129   1136                             1169    1177                                                                                                                             1306      1316                                                  
                                                          1036                                                                                                                                                                                                                                                                                                                                          

Chain B from PDB  Type:PROTEIN  Length:336
 aligned with PDK2_RAT | Q64536 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:364
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369    
            PDK2_RAT     10 NASLAGAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNCSVSDVVKDAYDMAKLLCDKYYMASPDLEIQEVNATNATQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLTLPPIKIMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPV  373
               SCOP domains d1jm6b1 B:1002-1169 Pyruvate de   hydrogenase kinase                                                                                                                           d1jm6b2 B:1177-1365 Pyruvate dehydrogenase kinase                                                                                                                                             SCOP domains
               CATH domains -1jm6B02 B:1003-1180  [code=1.2   0.140.20, no name defined]                                                                                                                       1jm6B01 B:1181-1361  [code=3.30.565.10, no name defined]                                                                                                                             ---- CATH domains
           Pfam domains (1) -------------------BCDHK_Adom3-   1jm6B03 B:1021-1185                                                                                                                                   ----------------------------------------------HATPase_c-1jm6B01 B:1232-1355                                                                                               ---------- Pfam domains (1)
           Pfam domains (2) -------------------BCDHK_Adom3-   1jm6B04 B:1021-1185                                                                                                                                   ----------------------------------------------HATPase_c-1jm6B02 B:1232-1355                                                                                               ---------- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhh.......hhhhhhh..---.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.-----------.hhhhhhhhhhhhhhhhhhhhhhhhhhh.-------.......eeeeehhhhhhhhhhhhhhhhhh.......eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeeee.....hhhhhhhhhh.........-------......hhhhhhhhhhhhh..eeeeeee...eeeeeeeee.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jm6 B 1002 NASLAGAPKYIEHFSKFSPSPLSMKQFLDFG---ACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEY-----------QNIQYFLDRFYLSRISIRMLINQHTLIFD-------PKHIGSIDPNCSVSDVVKDAYDMAKLLCDKYYMASPDLEIQEVNATNATQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLTLPPIKIMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTP-------PLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPV 1365
                                  1011      1021      1031|   | 1041      1051      1061      1071      1081      1091      1101      1111      1121       | -      1141      1151      1161       | -     |1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301    |    -  |   1321      1331      1341      1351      1361    
                                                       1032   |                                                                                         1129        1141                        1169    1177                                                                                                                             1306    1314                                                   
                                                           1036                                                                                                                                                                                                                                                                                                                                         

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PDK2_RAT | Q64536)
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: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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0004740    pyruvate dehydrogenase (acetyl-transferring) kinase activity    Catalysis of the reaction: ATP + pyruvate dehydrogenase (acetyl-transferring) = ADP + pyruvate dehydrogenase (acetyl-transferring) 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: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:0031670    cellular response to nutrient    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
    GO:0042593    glucose homeostasis    Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    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.
    GO:0010510    regulation of acetyl-CoA biosynthetic process from pyruvate    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate.
    GO:0010565    regulation of cellular ketone metabolic process    Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
    GO:0006111    regulation of gluconeogenesis    Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0010906    regulation of glucose metabolic process    Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
    GO:0006885    regulation of pH    Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell.
cellular component
    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:0005967    mitochondrial pyruvate dehydrogenase complex    Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA in eukaryotes; includes subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The This Eukaryotic form usually contains more subunits than its bacterial counterpart; for example, one known complex contains 30 E1 dimers, 60 E2 monomers, and 6 E3 dimers as well as a few copies of pyruvate dehydrogenase kinase and pyruvate dehydrogenase phosphatase.
    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.
    GO:0045254    pyruvate dehydrogenase complex    Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA; comprises subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3).

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDK2_RAT | Q645363crk 3crl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1JM6)