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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. L. De La Sierra-Gall B. Collinet, M. Graille, K. Blondeau, N. Bettache, A. Poupon, J. Janin Tilbeurgh
Date :  19 Nov 03  (Deposition) - 02 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Sam Dependent Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Leulliot, S. Quevillon-Cheruel, I. Sorel, I. L. 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

(-) Compounds

Molecule 1 - CARBOXY METHYL TRANSFERASE FOR PROTEIN PHOSPHATASE 2A CATALYTIC SUBUNIT
    Chains: A, B, C
    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

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1BME6Ligand/IonBETA-MERCAPTOETHANOL
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2GOL2Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:202 , PRO A:233 , TYR A:321BINDING SITE FOR RESIDUE BME A 335
2AC2SOFTWARECYS B:202 , PRO B:233 , TYR B:321BINDING SITE FOR RESIDUE BME B 335
3AC3SOFTWARECYS C:202 , TYR C:206BINDING SITE FOR RESIDUE BME C 335
4AC4SOFTWAREASP A:11 , SER A:14 , CYS A:15 , ALA A:66 , SER A:70 , MET A:74 , HOH A:357 , HOH A:381BINDING SITE FOR RESIDUE BME A 336
5AC5SOFTWARECYS B:15 , ALA B:66 , SER B:70 , MET B:74BINDING SITE FOR RESIDUE BME B 336
6AC6SOFTWARESER C:14 , CYS C:15 , ALA C:66 , SER C:70 , MET C:74BINDING SITE FOR RESIDUE BME C 336
7AC7SOFTWAREMET A:74 , ARG A:81 , TYR A:231 , GLN A:318 , TYR A:321BINDING SITE FOR RESIDUE GOL A 337
8AC8SOFTWAREHIS A:121BINDING SITE FOR RESIDUE GOL A 338

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:25 -Pro A:26
2Leu B:25 -Pro B:26
3Leu C:25 -Pro C:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 3)

Asymmetric Unit (1, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR435C1YDR435C.1IV:1333962-1332976987LCMT1_YEAST1-3283283A:9-328
B:4-328
C:7-328		320
325
322

(-) 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:321
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:321
                                                                                                                                                                                                                                                                                                                                                         328 
                                    18        28        38        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       308       318       328 
          LCMT1_YEAST     9 DYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW-   -
               SCOP domains d1rjfa_ A: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1rjfA00 A:9-329 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh..........hhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:9-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                              - Transcript 1
                 1rjf A   9 DYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQWH 329
                                    18        28        38        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       308       318       328 


Chain B from PDB  Type:PROTEIN  Length:327
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:327
                                                                                                                                                                                                                                                                                                                                                              328  
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323    |  
          LCMT1_YEAST     4 IIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW--   -
               SCOP domains d1rjfb_ B: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1rjfB00 B:4-330 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....hhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhh.eeeeeeeee........hhhhhhhhhhhhhh...........hhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:4-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                                   -- Transcript 1
                 1rjf B   4 IIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQWHH 330
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       


Chain C from PDB  Type:PROTEIN  Length:325
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:325
                                                                                                                                                                                                                                                                                                                                                           328   
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326 |   
          LCMT1_YEAST     7 QTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW---   -
               SCOP domains d1rjfc_ C: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1rjfC00 C:7-331 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) -----------------LCM-1rjfC01 C:24-220                                                                                                                                                                                 --------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------LCM-1rjfC02 C:24-220                                                                                                                                                                                 --------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------LCM-1rjfC03 C:24-220                                                                                                                                                                                 --------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..ee.eeeehhhhhhhhhhhhhhhhhhhhhhh..........eeee....eeee....hhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhh.eeeeeeeee........hhhhhhhhhh...............hhhhhhhhhh...eeeeeehhhhhhh..hhhhhhhhhhhh...hhhhhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:7-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                                --- Transcript 1
                 1rjf C   7 QTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQWHHH 331
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326
   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  (1, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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 1rjg 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
1rjg SAME PROTEIN, SPACEGROUP P 21 21 21