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(-) Description

Title :  PPM1 WITH 1,8-ANS
 
Authors :  M. R. Groves
Date :  18 Dec 06  (Deposition) - 30 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ppm1 In The Presence Of 1, 8-Ans, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Groves, I. B. Muller, X. Kreplin, J. Muller-Dieckmann
A Method For The General Identification Of Protein Crystals In Crystallization Experiments Using A Noncovalent Fluorescent Dye.
Acta Crystallogr. , Sect. D V. 63 526 2007
PubMed-ID: 17372358  |  Reference-DOI: 10.1107/S0907444906056137
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUCINE CARBOXYL METHYLTRANSFERASE 1
    Chains: A, B, C
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PETM11
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: PPM1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PROTEIN PHOSPHATASE METHYLTRANSFERASE 1

 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  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:16 , TYR B:41 , HIS B:45 , THR B:82 , ASP B:109 , LEU B:110 , ARG B:111 , HOH B:2064 , HOH B:2107BINDING SITE FOR RESIDUE PO4 B 2003
2AC2SOFTWARELYS C:16 , TYR C:41 , HIS C:45 , ASP C:109 , LEU C:110 , ARG C:111 , HOH C:2047 , HOH C:2051BINDING SITE FOR RESIDUE PO4 C 2004
3AC3SOFTWARELYS A:16 , TYR A:41 , HIS A:45 , ASP A:109 , LEU A:110 , ARG A:111 , HOH A:2042 , HOH A:2071 , HOH A:2352BINDING SITE FOR RESIDUE PO4 A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OB1)

(-) 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 2OB1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OB1)

(-) Exons   (1, 3)

Asymmetric Unit (1, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR435C1YDR435C.1IV:1333962-1332976987LCMT1_YEAST1-3283283A:10-328
B:10-328
C:10-328		319
319
319

(-) 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:319
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:319
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         
          LCMT1_YEAST    10 YDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
               SCOP domains d2ob1a_ A: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2ob1A00 A:10-328 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhh...........hhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh.eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:10-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                             Transcript 1
                 2ob1 A  10 YDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:319
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         
          LCMT1_YEAST    10 YDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
               SCOP domains d2ob1b_ B: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2ob1B00 B:10-328 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhh...........eeeee..eeeee....hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhhh...........hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:10-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                             Transcript 1
                 2ob1 B  10 YDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         


Chain C from PDB  Type:PROTEIN  Length:319
 aligned with LCMT1_YEAST | Q04081 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:319
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         
          LCMT1_YEAST    10 YDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
               SCOP domains d2ob1c_ C: Leucine carboxy methyltransferase Ppm1                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2ob1C00 C:10-328 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) --------------LCM-2ob1C01 C:24-220                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------LCM-2ob1C02 C:24-220                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) --------------LCM-2ob1C03 C:24-220                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------ Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....hhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhh.............hhhhhhhh.....eeeeeehhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh.eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:10-328 UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                                                                             Transcript 1
                 2ob1 C  10 YDALSCKLAAISVGYLPSSGLQRLSVDLSKKYTEWHRSYLITLKKFSRRAFGKVDKAMRSSFPVMNYGTYLRTVGIDAAILEFLVANEKVQVVNLGCGSDLRMLPLLQMFPHLAYVDIDYNESVELKNSILRESEILRISLGLSKEDTAKSPFLIDQGRYKLAACDLNDITETTRLLDVCTKREIPTIVISECLLCYMHNNESQLLINTIMSKFSHGLWISYDPIGGSQPNDRFGAIMQSNLKESRNLEMPTLMTYNSKEKYASRWSAAPNVIVNDMWEIFNAQIPESERKRLRSLQFLDELEELKVMQTHYILMKAQW 328
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319
   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  (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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  2ob1
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2ob2 PPM1 IN THE ABSENCE OF 1,8-ANS (CF 1JD)