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(-) Description

Title :  STRUCTURE OF PPM1, A LEUCINE CARBOXY METHYLTRANSFERASE INVOLVED IN THE REGULATION OF PROTEIN PHOSPHATASE 2A ACTIVITY
 
Authors :  N. Leulliot, S. Quevillon-Cheruel, I. Sorel, I. Li De La Sierra- Gallay, B. Collinet, M. Graille, K. Blondeau, N. Bettache, A. Poupon, J. Janin, H. Van Tilbeurgh
Date :  19 Nov 03  (Deposition) - 02 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym./Biol. Unit :  A
Keywords :  Sam Dependent Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Leulliot, S. Quevillon-Cheruel, I. Sorel, I. Li De La Sierra-Gallay, B. Collinet, M. Graille, K. Blondeau, N. Bettache, A. Poupon, J. Janin, H. Van Tilbeurgh
Structure Of Protein Phosphatase Methyltransferase 1 (Ppm1), A Leucine Carboxyl Methyltransferase Involved In The Regulation Of Protein Phosphatase 2A Activity
J. Biol. Chem. V. 279 8351 2004
PubMed-ID: 14660564  |  Reference-DOI: 10.1074/JBC.M311484200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOXY METHYL TRANSFERASE FOR PROTEIN PHOSPHATASE 2A CATALYTIC SUBUNIT
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9
    Expression System Strain: XL-10 GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PPM1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PPM1P

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , ALA A:12 , ARG A:81 , GLY A:105 , CYS A:106 , ASP A:128 , TYR A:129 , SER A:132 , CYS A:174 , ASP A:175 , LEU A:176 , ASN A:177 , GLU A:201 , CYS A:202 , LEU A:203 , HOH A:339 , HOH A:347BINDING SITE FOR RESIDUE SAH A 335

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:25 -Pro A:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR435C1YDR435C.1IV:1333962-1332976987LCMT1_YEAST1-3283281A:8-328 (gaps)321

(-) 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:291
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:324
                                                                                                                                                                                                                                                                                                                                                          328   
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327|   
          LCMT1_YEAST     8 TDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW---   -
               SCOP domains d1rjga_ A: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1rjgA00 A:8-331 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------LCM-1rjgA01 A:24-220                                                                                                                                                                                 --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhh.................eeeee....hhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhh.eeeeeeeee.---------------------------------hhhhhhh.....eeeeeehhhhhhhh.hhhhhhhhhhhh....hhhhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:8-328 (gaps) UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                        --- Transcript 1
                 1rjg A   8 TDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPI---------------------------------KEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQWHHH 331
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227      |  -         -         -         -|      277       287       297       307       317       327    
                                                                                                                                                                                                                                                            234                               268
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LCMT1_YEAST | Q04081)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0018423    protein C-terminal leucine carboxyl O-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + protein L-leucine = S-adenosyl-L-homocysteine + protein L-leucine methyl ester. This modification occurs only at the oxygen atoms of the free alpha carboxyl group of a leucine residue at the C-terminus of the protein.
    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:0006481    C-terminal protein methylation    The methylation of the C-terminal amino acid of a protein.
    GO:0043623    cellular protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LCMT1_YEAST | Q04081: 1rjd 1rje 1rjf 2ob1 2ob2

(-) Related Entries Specified in the PDB File

1rjd SAME PROTEIN COMPLEXED WITH S-ADENOSYLMETHIONINE
1rje SAME PROTEIN COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE
1rjf SAME PROTEIN COMPLEXED WITH GLYCEROL