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(-) Description

Title :  CRYSTAL STRUCTURE OF BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE PHOSPHATASE WITH MG (II) IONS AT THE ACTIVE SITE
 
Authors :  C. A. Brautigam, J. L. Chuang, D. T. Chuang
Date :  12 Jan 12  (Deposition) - 08 Feb 12  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  A
Keywords :  Metal-Ion-Assisted Catalysis, Dehydrogenase Phosphatase, Mitochondria, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. M. Wynn, J. Li, C. A. Brautigam, J. L. Chuang, D. T. Chuang
Structural And Biochemical Characterization Of Human Mitochondrial Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase.
J. Biol. Chem. V. 287 9178 2012
PubMed-ID: 22291014  |  Reference-DOI: 10.1074/JBC.M111.314963

(-) Compounds

Molecule 1 - PROTEIN PHOSPHATASE 1K, MITOCHONDRIAL
    ChainsA
    EC Number3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentTRUNCATED PHOSPHATASE PROTEIN (UNP RESIDUES 84-360)
    GenePPM1K, PP2CM
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPP2C DOMAIN-CONTAINING PROTEIN PHOSPHATASE 1K, PP2C-LIKE MITOCHONDRIAL PROTEIN, PP2C-TYPE MITOCHONDRIAL PHOSPHOPROTEIN PHOSPHATASE, PTMP, PROTEIN PHOSPHATASE 2C ISOFORM KAPPA, PP2C-KAPPA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1BME3Ligand/IonBETA-MERCAPTOETHANOL
2MG3Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:95 , CYS A:97 , PHE A:113 , ASN A:320BINDING SITE FOR RESIDUE BME A 501
2AC2SOFTWARECYS A:145 , ASP A:148 , GLU A:166BINDING SITE FOR RESIDUE BME A 502
3AC3SOFTWARECYS A:316 , GLU A:321BINDING SITE FOR RESIDUE BME A 503
4AC4SOFTWAREASP A:127 , ASP A:298 , ASP A:337 , HOH A:601 , HOH A:636 , HOH A:638BINDING SITE FOR RESIDUE MG A 504
5AC5SOFTWAREASP A:127 , GLY A:128 , HOH A:602 , HOH A:620 , HOH A:635 , HOH A:636BINDING SITE FOR RESIDUE MG A 505
6AC6SOFTWAREASP A:112 , GLU A:143 , HOH A:612 , HOH A:613 , HOH A:614 , HOH A:615BINDING SITE FOR RESIDUE MG A 506

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:214 -A:310

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DA1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030691N94KPPM1K_HUMANPolymorphism17853762AN94K
2UniProtVAR_050621E321KPPM1K_HUMANPolymorphism35523553AE321K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.PPM1K_HUMAN94-346  1A:94-346
2PPM_1PS01032 PPM-type phosphatase domain signature.PPM1K_HUMAN122-130  1A:122-130

(-) Exons   (0, 0)

(no "Exon" information available for 4DA1)

(-) 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:257
 aligned with PPM1K_HUMAN | Q8N3J5 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:260
                                    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
          PPM1K_HUMAN    90 ISLENVGCASQIGKRKENEDRFDFAQLTDEVLYFAVYDGHGGPAAADFCHTHMEKCIMDLLPKEKNLETLLTLAFLEIDKAFSSHARLSADATLLTSGTTATVALLRDGIELVVASVGDSRAILCRKGKPMKLTIDHTPERKDEKERIKKCGGFVAWNSLGQPHVNGRLAMTRSIGDLDLKTSGVIAEPETKRIKLHHADDSFLVLTTDGINFMVNSQEICDFVNQCHDPNEAAHAVTEQAIQYGTEDNSTAVVVPFGAW 349
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeeee........eeeeeee....eeeeeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.ee.eeeeeee...eeeeeee...eeeeee..eeee........hhhhhhhhhhhh..ee..---..ee.........ee.hhhhhhh.....eeeeee......eeeeeehhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----K----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K---------------------------- SAPs(SNPs)
                PROSITE (1) ----PPM_2  PDB: A:94-346 UniProt: 94-346                                                                                                                                                                                                                         --- PROSITE (1)
                PROSITE (2) --------------------------------PPM_1    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4da1 A  90 ISLENVGCASQIGKRKENEDRFDFAQLTDEVLYFAVYDGHGGPAAADFCHTHMEKCIMDLLPKEKNLETLLTLAFLEIDKAFSSHARLSADATLLTSGTTATVALLRDGIELVVASVGDSRAILCRKGKPMKLTIDHTPERKDEKERIKKCGGFVAWN---QPHVNGRLAMTRSIGDLDLKTSGVIAEPETKRIKLHHADDSFLVLTTDGINFMVNSQEICDFVNQCHDPNEAAHAVTEQAIQYGTEDNSTAVVVPFGAW 349
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       | - |     259       269       279       289       299       309       319       329       339       349
                                                                                                                                                                                       247 251                                                                                                  

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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  (0, 0)

(no "SCOP Domain" information available for 4DA1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DA1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DA1)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPM1K_HUMAN | Q8N3J5)
molecular function
    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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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: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: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

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        PPM1K_HUMAN | Q8N3J52iq1

(-) Related Entries Specified in the PDB File

2iq1