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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN L-ISOASPARTYL METHYLTRANSFERASE
 
Authors :  C. Ryttersgaard, S. C. Griffith, M. R. Sawaya, D. C. Maclaren, S. Clarke, T. O. Yeates
Date :  08 Jan 02  (Deposition) - 08 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann-Fold Doubly-Wound-Alpha-Beta-Alpha-Sandwich, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Ryttersgaard, S. C. Griffith, M. R. Sawaya, D. C. Maclaren, S. Clarke, T. O. Yeates
Crystal Structure Of Human L-Isoaspartyl Methyltransferase.
J. Biol. Chem. V. 277 10642 2002
PubMed-ID: 11792715  |  Reference-DOI: 10.1074/JBC.M200229200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
    ChainsA
    EC Number2.1.1.77
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDM2X
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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
1AC1SOFTWAREALA A:56 , THR A:57 , ILE A:58 , SER A:59 , HIS A:64 , GLY A:85 , SER A:86 , GLY A:87 , SER A:88 , ASP A:109 , HIS A:110 , LEU A:114 , GLY A:140 , ASP A:141 , GLY A:142 , ARG A:143 , GLY A:158 , PRO A:214 , LEU A:215 , THR A:216 , GLN A:221 , HOH A:301 , HOH A:304BINDING SITE FOR RESIDUE SAH A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KR5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:150 -Pro A:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006173V120IPIMT_HUMANPolymorphism4816AV119I

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PCMTPS01279 Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature.PIMT_HUMAN141-156  1A:140-155

(-) Exons   (0, 0)

(no "Exon" information available for 1KR5)

(-) 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:218
 aligned with PIMT_HUMAN | P22061 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:218
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217        
           PIMT_HUMAN     8 ASHSELIHNLRKNGIIKTDKVFEVMLATDRSHYAKCNPYMDSPQSIGFQATISAPHMHAYALELLFDQLHEGAKALDVGSGSGILTACFARMVGCTGKVIGIDHIKELVDDSVNNVRKDDPTLLSSGRVQLVVGDGRMGYAEEAPYDAIHVGAAAPVVPQALIDQLKPGGRLILPVGPAGGNQMLEQYDKLQDGSIKMKPLMGVIYVPLTDKEKQWSR 225
               SCOP domains d1kr5a_ A: Protein-L-isoaspartyl O-methyltransferase                                                                                                                                                                       SCOP domains
               CATH domains 1kr5A00 A:7-224 Vaccinia Virus protein VP39                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....hhhhhhhhhhhhhhhh..........ee.....ee.hhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeee......eeeeeeee.....eeeeeeeee......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------I--------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------PCMT            --------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kr5 A   7 ASHSELIHNLRKNGIIKTDKVFEVMLATDRSHYAKCNPYMDSPQSIGFQATISAPHMHAYALELLFDQLHEGAKALDVGSGSGILTACFARMVGCTGKVIGIDHIKELVDDSVNNVRKDDPTLLSSGRVQLVVGDGRMGYAEEAPYDAIHVGAAAPVVPQALIDQLKPGGRLILPVGPAGGNQMLEQYDKLQDGSIKMKPLMGVIYVPLTDKEKQWSR 224
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KR5)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PIMT_HUMAN | P22061)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0004719    protein-L-isoaspartate (D-aspartate) O-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + protein L-beta-aspartate = S-adenosyl-L-homocysteine + protein L-beta-aspartate methyl ester.
    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:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    GO:0030091    protein repair    The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.

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 Related Entries

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

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        PIMT_HUMAN | P220611i1n

(-) Related Entries Specified in the PDB File

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