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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 :  1.80
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 (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, 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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1BME6Ligand/IonBETA-MERCAPTOETHANOL
2SAM3Ligand/IonS-ADENOSYLMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG C:192 , SER C:224 , HIS C:330 , HIS C:331 , HIS C:332 , HIS C:333 , HIS C:334BINDING SITE FOR RESIDUE SO4 C 335
02AC2SOFTWAREILE A:5 , GLN A:6 , THR A:8 , ASP A:9 , ALA A:12 , ARG A:81 , GLY A:105 , CYS A:106 , GLY A:107 , ASP A:128 , TYR A:129 , CYS A:174 , ASP A:175 , LEU A:176 , ASN A:177 , GLU A:201 , CYS A:202 , LEU A:203 , HOH A:810 , HOH A:811 , HOH A:838 , HOH A:864 , HOH A:913 , HOH A:1010BINDING SITE FOR RESIDUE SAM A 801
03AC3SOFTWAREILE B:5 , GLN B:6 , THR B:8 , ASP B:9 , ALA B:12 , ARG B:81 , GLY B:105 , CYS B:106 , GLY B:107 , ASP B:128 , TYR B:129 , CYS B:174 , ASP B:175 , LEU B:176 , ASN B:177 , GLU B:201 , CYS B:202 , LEU B:203 , TYR B:206 , HOH B:809 , HOH B:811 , HOH B:823 , HOH B:847 , HOH B:863 , HOH B:877BINDING SITE FOR RESIDUE SAM B 802
04AC4SOFTWAREILE C:5 , GLN C:6 , THR C:8 , ALA C:12 , ARG C:81 , GLY C:105 , CYS C:106 , GLY C:107 , ASP C:128 , TYR C:129 , CYS C:174 , ASP C:175 , LEU C:176 , ASN C:177 , GLU C:201 , CYS C:202 , LEU C:203 , TYR C:206 , HOH C:824 , HOH C:826 , HOH C:846 , HOH C:869 , HOH C:912 , HOH C:949BINDING SITE FOR RESIDUE SAM C 803
05AC5SOFTWARECYS A:202 , TYR A:206 , PRO A:233 , MET A:259BINDING SITE FOR RESIDUE BME A 804
06AC6SOFTWARECYS B:202 , TYR B:206 , PRO B:233 , HOH B:978BINDING SITE FOR RESIDUE BME B 805
07AC7SOFTWARECYS C:202 , TYR C:206 , PRO C:233 , MET C:259BINDING SITE FOR RESIDUE BME C 806
08AC8SOFTWARESER A:14 , CYS A:15 , ALA A:66 , SER A:70 , HOH A:960BINDING SITE FOR RESIDUE BME A 807
09AC9SOFTWARECYS B:15 , ALA B:66 , SER B:70 , MET B:74BINDING SITE FOR RESIDUE BME B 808
10BC1SOFTWARECYS C:15 , ALA C:66 , SER C:70 , MET C:74 , HOH C:1026BINDING SITE FOR RESIDUE BME C 809

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Leu A:25 -Pro A:26
2Ser A:160 -Pro A:161
3Leu B:25 -Pro B:26
4Ser B:160 -Pro B:161
5Leu C:25 -Pro C:26
6Ser C:160 -Pro C:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 3)

Asymmetric Unit (1, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR435C1YDR435C.1IV:1333962-1332976987LCMT1_YEAST1-3283283A:2-328
B:2-328
C:2-328		327
327
327

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

    Alignment length:328
                                                                                                                                                                                                                                                                                                                                                                328 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      | 
          LCMT1_YEAST     2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW-   -
               SCOP domains d1rjda_ A: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1rjdA00 A:2-329 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhh..........eeee...eeeee....hhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh..........hhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhh.....hhhhhhhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                                     - Transcript 1
                 1rjd A   2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQWH 329
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321        


Chain B from PDB  Type:PROTEIN  Length:329
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:329
                                                                                                                                                                                                                                                                                                                                                                328  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      |  
          LCMT1_YEAST     2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW--   -
               SCOP domains d1rjdb_ B: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1rjdB00 B:2-330 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhh...........eeeee..eeeee....hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee........hhhhhhhhhhhhhhh..........hhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                                     -- Transcript 1
                 1rjd B   2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQWHH 330
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321         


Chain C from PDB  Type:PROTEIN  Length:333
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:333
                                                                                                                                                                                                                                                                                                                                                                328      
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      |  -   
          LCMT1_YEAST     2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW------   -
               SCOP domains d1rjdc_ C: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1rjdC00 C:2-334 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ----------------------LCM-1rjdC01 C:24-220                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------LCM-1rjdC02 C:24-220                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) ----------------------LCM-1rjdC03 C:24-220                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------------ Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhh...........eeeee..eeeee....hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee........hhhhhhhhhhhhhhh..........hhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhh.....hhhhhhhhhh.eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:2-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                                     ------ Transcript 1
                 1rjd C   2 ERIIQQTDYDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQWHHHHHH 334
                                    11        21        31        41        51        61        71        81        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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 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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  1rjd
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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