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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN L-ISOASPARTATE O-METHYLTRANSFERASE HOMOLOGUE FROM SULFOLOBUS TOKODAII
 
Authors :  Y. Tanaka, K. Tsumoto, Y. Yasutake, M. Umetsu, M. Yao, I. Tanaka, H. Fuka I. Kumagai
Date :  25 Feb 04  (Deposition) - 10 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  C,D  (3x)
Keywords :  Trimeric Coiled Coil Assembly, Inter-Subunit Disulfide Bridge, Protein Repair Enzyme, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Tanaka, K. Tsumoto, Y. Yasutake, M. Umetsu, M. Yao, H. Fukada, I. Tanaka, I. Kumagai
How Oligomerization Contributes To The Thermostability Of A Archaeon Protein: Protein L-Isoaspartyl-O-Methyltransferase From Sulfolobus Tokodaii
J. Biol. Chem. V. 279 32957 2004
PubMed-ID: 15169774  |  Reference-DOI: 10.1074/JBC.M404405200

(-) Compounds

Molecule 1 - 231AA LONG HYPOTHETICAL PROTEIN-L-ISOASPARTATE O- METHYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.1.1.77
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ST1123
    Organism Scientific: SULFOLOBUS TOKODAII
    Organism Taxid: 111955
    Synonym: PROTEIN L-ISOASPARTATE O-METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): AB  
Biological Unit 2 (3x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VBF)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:149 -B:149
2C:149 -D:149

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VBF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VBF)

(-) 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:224
 aligned with Q972K9_SULTO | Q972K9 from UniProtKB/TrEMBL  Length:231

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
         Q972K9_SULTO     1 MSEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYAHTHEALPILPGINTTALNLGIFMLDELDLHKGQKVLEIGTGIGYYTALIAEIVDKVVSVEINEKMYNYASKLLSYYNNIKLILGDGTLGYEEEKPYDRVVVWATAPTLLCKPYEQLKEGGIMILPIGVGRVQKLYKVIKKGNSPSLENLGEVMFGRIGGLYGFYDDYDDIEFRVNKLERQIKSIL 224
               SCOP domains d1vbfa_ A: Protein-L-isoaspartyl O-methyltransferase                                                                                                                                                                             SCOP domains
               CATH domains 1vbfA00 A:1-224 Vaccinia Virus protein VP39                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......eeee..eee.hhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhhh....eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeee.....eeeeeee......eeeeeeee................hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbf A   1 ASEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYAHTHEALPILPGINTTALNLGIFmLDELDLHKGQKVLEIGTGIGYYTALIAEIVDKVVSVEINEKmYNYASKLLSYYNNIKLILGDGTLGYEEEKPYDRVVVWATAPTLLCKPYEQLKEGGImILPIGVGRVQKLYKVIKKGNSPSLENLGEVmFGRIGGLYGFYDDYDDIEFRVNKLERQIKSIL 224
                                    10        20        30        40        50        60 |      70        80        90       100   |   110       120       130       140       150       160|      170       180       190 |     200       210       220    
                                                                                        62-MSE                                   104-MSE                                                  161-MSE                        192-MSE                            


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with Q972K9_SULTO | Q972K9 from UniProtKB/TrEMBL  Length:231

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
         Q972K9_SULTO     1 MSEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYAHTHEALPILPGINTTALNLGIFMLDELDLHKGQKVLEIGTGIGYYTALIAEIVDKVVSVEINEKMYNYASKLLSYYNNIKLILGDGTLGYEEEKPYDRVVVWATAPTLLCKPYEQLKEGGIMILPIGVGRVQKLYKVIKKGNSPSLENLGEVMFGRIGGLYGFYDDYDDIEFRVNKLERQIKSILDN 226
               SCOP domains d1vbfb_ B: Protein-L-isoaspartyl O-methyltransferase                                                                                                                                                                               SCOP domains
               CATH domains 1vbfB00 B:1-226 Vaccinia Virus protein VP39                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhh.......eeee..eee.hhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhh.......eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeee.....eeeeeee......eeeeeeee................hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbf B   1 ASEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYAHTHEALPILPGINTTALNLGIFmLDELDLHKGQKVLEIGTGIGYYTALIAEIVDKVVSVEINEKmYNYASKLLSYYNNIKLILGDGTLGYEEEKPYDRVVVWATAPTLLCKPYEQLKEGGImILPIGVGRVQKLYKVIKKGNSPSLENLGEVmFGRIGGLYGFYDDYDDIEFRVNKLERQIKSILDN 226
                                    10        20        30        40        50        60 |      70        80        90       100   |   110       120       130       140       150       160|      170       180       190 |     200       210       220      
                                                                                        62-MSE                                   104-MSE                                                  161-MSE                        192-MSE                              


Chain C from PDB  Type:PROTEIN  Length:224
 aligned with Q972K9_SULTO | Q972K9 from UniProtKB/TrEMBL  Length:231

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
         Q972K9_SULTO     1 MSEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYAHTHEALPILPGINTTALNLGIFMLDELDLHKGQKVLEIGTGIGYYTALIAEIVDKVVSVEINEKMYNYASKLLSYYNNIKLILGDGTLGYEEEKPYDRVVVWATAPTLLCKPYEQLKEGGIMILPIGVGRVQKLYKVIKKGNSPSLENLGEVMFGRIGGLYGFYDDYDDIEFRVNKLERQIKSIL 224
               SCOP domains d1vbfc_ C: Protein-L-isoaspartyl O-methyltransferase                                                                                                                                                                             SCOP domains
               CATH domains 1vbfC00 C:1-224 Vaccinia Virus protein VP39                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhh.......eeee..eee.hhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhh....eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeee.....eeeeeee......eeeeeeee................hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbf C   1 ASEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYAHTHEALPILPGINTTALNLGIFmLDELDLHKGQKVLEIGTGIGYYTALIAEIVDKVVSVEINEKmYNYASKLLSYYNNIKLILGDGTLGYEEEKPYDRVVVWATAPTLLCKPYEQLKEGGImILPIGVGRVQKLYKVIKKGNSPSLENLGEVmFGRIGGLYGFYDDYDDIEFRVNKLERQIKSIL 224
                                    10        20        30        40        50        60 |      70        80        90       100   |   110       120       130       140       150       160|      170       180       190 |     200       210       220    
                                                                                        62-MSE                                   104-MSE                                                  161-MSE                        192-MSE                            


Chain D from PDB  Type:PROTEIN  Length:224
 aligned with Q972K9_SULTO | Q972K9 from UniProtKB/TrEMBL  Length:231

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
         Q972K9_SULTO     1 MSEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYAHTHEALPILPGINTTALNLGIFMLDELDLHKGQKVLEIGTGIGYYTALIAEIVDKVVSVEINEKMYNYASKLLSYYNNIKLILGDGTLGYEEEKPYDRVVVWATAPTLLCKPYEQLKEGGIMILPIGVGRVQKLYKVIKKGNSPSLENLGEVMFGRIGGLYGFYDDYDDIEFRVNKLERQIKSIL 224
               SCOP domains d1vbfd_ D: Protein-L-isoaspartyl O-methyltransferase                                                                                                                                                                             SCOP domains
               CATH domains 1vbfD00 D:1-224 Vaccinia Virus protein VP39                                                                                                                                                                                      CATH domains
           Pfam domains (1) -PCMT-1vbfD01 D:2-199                                                                                                                                                                                  ------------------------- Pfam domains (1)
           Pfam domains (2) -PCMT-1vbfD02 D:2-199                                                                                                                                                                                  ------------------------- Pfam domains (2)
           Pfam domains (3) -PCMT-1vbfD03 D:2-199                                                                                                                                                                                  ------------------------- Pfam domains (3)
           Pfam domains (4) -PCMT-1vbfD04 D:2-199                                                                                                                                                                                  ------------------------- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eee.hhhhhhhhhhhh......eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh..eeeee.hhhhh......eeeeee.......hhhhhhheeeeeeeeeee.....eeeeeee......eeeeeeee................hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbf D   1 ASEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYAHTHEALPILPGINTTALNLGIFmLDELDLHKGQKVLEIGTGIGYYTALIAEIVDKVVSVEINEKmYNYASKLLSYYNNIKLILGDGTLGYEEEKPYDRVVVWATAPTLLCKPYEQLKEGGImILPIGVGRVQKLYKVIKKGNSPSLENLGEVmFGRIGGLYGFYDDYDDIEFRVNKLERQIKSIL 224
                                    10        20        30        40        50        60 |      70        80        90       100   |   110       120       130       140       150       160|      170       180       190 |     200       210       220    
                                                                                        62-MSE                                   104-MSE                                                  161-MSE                        192-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q972K9_SULTO | Q972K9)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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.

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