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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANS-ACONITATE METHYLTRANSFERASE FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  C. Chang, X. Xu, H. Zheng, A. Savchenko, A. M. Edwards, A. Joachimiak, Mi Center For Structural Genomics (Mcsg)
Date :  08 Mar 07  (Deposition) - 10 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trans-Aconitate Methyltransferase, Sam Dependent Methyltransferase, Agrobacterium Tumefaciens, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, X. Xu, H. Zheng, A. Savchenko, A. Joachimiak
Crystal Structure Of Trans-Aconitate Methyltransferase From Agrobacterium Tumefaciens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANS-ACONITATE 2-METHYLTRANSFERASE
    Atcc: 33970
    Chains: A, B
    EC Number: 2.1.1.144
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET DERIVATIVE
    Expression System Strain: BL21(DE3) DERIVATIVE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TAM, ATU0870, AGR_C_1589
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:38 , GLY A:40 , SER A:44 , ASP A:61 , SER A:62 , ASP A:63 , MSE A:66 , ALA A:82 , ASP A:83 , LEU A:84 , ASN A:99 , ALA A:100 , VAL A:101 , HOH A:330 , HOH A:346 , HOH A:365 , HOH A:479BINDING SITE FOR RESIDUE SAH A 301
2AC2SOFTWAREGLY B:38 , GLY B:40 , SER B:44 , ASP B:61 , SER B:62 , ASP B:63 , MSE B:66 , ALA B:82 , ASP B:83 , LEU B:84 , ASN B:99 , ALA B:100 , VAL B:101 , HOH B:305 , HOH B:366 , HOH B:406BINDING SITE FOR RESIDUE SAH B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P35)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P35)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P35)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P35)

(-) Exons   (0, 0)

(no "Exon" information available for 2P35)

(-) 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:245
 aligned with TAM_AGRFC | Q8UH15 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:252
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  
            TAM_AGRFC     5 AQQYLKFEDERTRPARDLLAQVPLERVLNGYDLGCGPGNSTELLTDRYGVNVITGIDSDDDMLEKAADRLPNTNFGKADLATWKPAQKADLLYANAVFQWVPDHLAVLSQLMDQLESGGVLAVQMPDNLQEPTHIAMHETADGGPWKDAFSGGGLRRKPLPPPSDYFNALSPKSSRVDVWHTVYNHPMKDADSIVEWVKGTGLRPYLAAAGEENREAFLADYTRRIAAAYPPMADGRLLLRFPRLFVVAVKK 256
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2p35A01 A:5-130,A:162-190,A:238-256 Vaccinia Virus protein VP39                                                               2p35A02                 -------2p35A01                      2p35A02 A:131-154,A:191-236                   -2p35A01             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh...hhhhhhhhhhhh.........eeee....hhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeee...........eeeeeee.hhhhh.hhhhhhhhhh..eeeeeeeeeeee....hhhhhhhhhhhhhh.hhhhh-------....hhhhhhhhhh..eeeeeeeeeeeeeee.hhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2p35 A   5 AQQYLKFEDERTRPARDLLAQVPLERVLNGYDLGCGPGNSTELLTDRYGVNVITGIDSDDDmLEKAADRLPNTNFGKADLATWKPAQKADLLYANAVFQWVPDHLAVLSQLmDQLESGGVLAVQmPDNLQEPTHIAmHETADGGPWKDAF-------KPLPPPSDYFNALSPKSSRVDVWHTVYNHPmKDADSIVEWVKGTGLRPYLAAAGEENREAFLADYTRRIAAAYPPmADGRLLLRFPRLFVVAVKK 256
                                    14        24        34        44        54        64 |      74        84        94       104       114 |     124    |  134      |144       154       164       174       184       194       204       214       224       234  |    244       254  
                                                                                        66-MSE                                           116-MSE      129-MSE     141-MSE      154     162                           192-MSE                                      237-MSE               


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with TAM_AGRFC | Q8UH15 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:245
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
            TAM_AGRFC    12 EDERTRPARDLLAQVPLERVLNGYDLGCGPGNSTELLTDRYGVNVITGIDSDDDMLEKAADRLPNTNFGKADLATWKPAQKADLLYANAVFQWVPDHLAVLSQLMDQLESGGVLAVQMPDNLQEPTHIAMHETADGGPWKDAFSGGGLRRKPLPPPSDYFNALSPKSSRVDVWHTVYNHPMKDADSIVEWVKGTGLRPYLAAAGEENREAFLADYTRRIAAAYPPMADGRLLLRFPRLFVVAVKK 256
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2p35B01 B:12-130,B:161-190,B:238-256 Vaccinia Virus protein VP39                                                       2p35B02                  -----2p35B01                       2p35B02 B:131-155,B:191-236                   -2p35B01             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh........eeee....hhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeee...........eeeeeee.hhhhh.hhhhhhhhhhh.eeeeeeeeeeee....hhhhhhhhhhhhhh.hhhhhh-----.....hhhhhhhhhh..eeeeeeeeeeeeeee.hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhh.......eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p35 B  12 EDERTRPARDLLAQVPLERVLNGYDLGCGPGNSTELLTDRYGVNVITGIDSDDDmLEKAADRLPNTNFGKADLATWKPAQKADLLYANAVFQWVPDHLAVLSQLmDQLESGGVLAVQmPDNLQEPTHIAmHETADGGPWKDAFS-----RKPLPPPSDYFNALSPKSSRVDVWHTVYNHPmKDADSIVEWVKGTGLRPYLAAAGEENREAFLADYTRRIAAAYPPmADGRLLLRFPRLFVVAVKK 256
                                    21        31        41        51        61    |   71        81        91       101       111    |  121       131       141       151   |   161       171       181       191|      201       211       221       231     | 241       251     
                                                                                 66-MSE                                           116-MSE      129-MSE     141-MSE       155   161                            192-MSE                                      237-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 2P35)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2P35)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TAM_AGRFC | Q8UH15)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0030798    trans-aconitate 2-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + trans-aconitate = (E)-3-(methoxycarbonyl)pent-2-enedioate + S-adenosyl-L-homocysteine.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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