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(-) Description

Title :  CRYSTAL STRUCTURE OF NATIVE BOVINE PDP1C
 
Authors :  Y. Guo, S. R. Ernst, D. W. Carroll, Hackert M. L.
Date :  27 Apr 10  (Deposition) - 18 May 11  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphatase, Pdp1C, Pyruvate Dehydrogenase Phosphatase 1, Pyruvate Dehydrogenase Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Guo, S. R. Ernst, D. W. Carroll, M. L. Hackert
Crystal Structure Of Catalytic Subunit Of Bovine Pyruvate Dehydrogenase Phophatase
To Be Published 2010
PubMed: search

(-) Compounds

Molecule 1 - PYRUVATE DEHYDROGENASE PHOSPHATASE 1
    Chains: A
    EC Number: 3.1.3.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK233-3
    Expression System Strain: JM 101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PDP1C, UNP RESIDUES 72-538
    Gene: PDP1
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: PDP 1, PYRUVATE DEHYDROGENASE PHOSPHATASE CATALYTIC SUBUNIT 1, PDPC 1, PROTEIN PHOSPHATASE 2C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:73 , GLY A:74 , GLU A:230BINDING SITE FOR RESIDUE MN A 501
2AC2SOFTWAREASP A:73 , GLU A:230 , ASP A:347 , ASP A:445 , HOH A:504BINDING SITE FOR RESIDUE MN A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MQ3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:321 -Pro A:322

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MQ3)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.PDP1_BOVIN109-525  1A:38-454
2PPM_1PS01032 PPM-type phosphatase domain signature.PDP1_BOVIN139-147  1A:68-76

(-) Exons   (0, 0)

(no "Exon" information available for 3MQ3)

(-) 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:378
 aligned with PDP1_BOVIN | P35816 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:453
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531   
           PDP1_BOVIN    82 PPQVNSILKANEYSFKVPEFDGKNVSSVLGFDSNQLPANAPIEDRRSAATCLQTRGMLLGVFDGHAGCACSQAVSERLFYYIAVSLLPHETLLEIENAVESGRALLPILQWHKHPNDYFSKEASKLYFNSLRTYWQELIDLNTGESTDIDVKEALINAFKRLDNDISLEAQVGDPNSFLNYLVLRVAFSGATACVAHVDGVDLHVANTGDSRAMLGVQEEDGSWSAVTLSNDHNAQNEREVERLKLEHPKNEAKSVVKQDRLLGLLMPFRAFGDVKFKWSIDLQKRVIESGPDQLNDNEYTKFIPPNYYTPPYLTAEPEVTYHRLRPQDKFLVLATDGLWETMHRQDVVRIVGEYLTGMHHQQPIAVGGYKVTLGQMHGLLTERRAKMSSVFEDQNAATHLIRHAVGNNEFGAVDHERLSKMLSLPEELARMYRDDITIIVVQFNSHVVGAYQ 534
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------      --------PP2C-3mq3A01 A:123-415                                                                                                                                                                                                                                                                               -              --------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...eeee...........eeeeeeeee.......eeeeeeee.....eeeeeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh------....eee...........hhhhhhhhhhhhhhhhhh--------.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhee.eeeeeee..eeeeeee...eeeeeee.....eeeee........hhhhhhhhhhhhhhhhh...ee..ee.........ee.hhhh.hhhhhhhhh.------------.................eeeeee....eeeeeeehhhhhh..hhhhhhhhhhhhhh..-----------------------------------.hhhhhhhhhhh--------------........hhhhh...eeeeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------PPM_2  PDB: A:38-454 UniProt: 109-525                                                                                                                                                                                                                                                                                                                                                                                            --------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------PPM_1    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mq3 A  11 PPQVNSILKANEYSFKVPEFDGKNVSSVLGFDSNQLPANAPIEDRRSAATCLQTRGMLLGVFDGHAGCACSQAVSERLFYYIAVSLLPHETLLEIENA------LLPILQWHKHPNDYFSKEASKLYFNSLRTYWQELID--------IDVKEALINAFKRLDNDISLEAQVGDPNSFLNYLVLRVAFSGATACVAHVDGVDLHVANTGDSRAMLGVQEEDGSWSAVTLSNDHNAQNEREVERLKLEHPKNEAKSVVKQDRLLGLLMPFRAFGDVKFKWSIDLQKRVIE------------KFIPPNYYTPPYLTAEPEVTYHRLRPQDKFLVLATDGLWETMHRQDVVRIVGEYLTGM-----------------------------------QNAATHLIRHAV--------------KMLSLPEELARMYRDDITIIVVQFNSHVVGAYQ 463
                                    20        30        40        50        60        70        80        90       100       | -    |  120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290        |-         - |     320       330       340       350       360        |-         -         -         -    |  410     |   -         -|      440       450       460   
                                                                                                                           108    115                                150      159                                                                                                                                         299          312                                                      369                                 405        416            431
   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  (0, 0)

(no "SCOP Domain" information available for 3MQ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MQ3)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PP2C (22)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PDP1_BOVIN | P35816)
molecular function
    GO:0004741    [pyruvate dehydrogenase (lipoamide)] phosphatase activity    Catalysis of the reaction: [pyruvate dehydrogenase (lipoamide)] phosphate + H2O = [pyruvate dehydrogenase (lipoamide)] + phosphate.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0004722    protein serine/threonine phosphatase activity    Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
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: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
        PDP1_BOVIN | P35816: 3n3c

(-) Related Entries Specified in the PDB File

3n3c