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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A METHYLTRANSFERASE DOMAIN FROM BACTEROIDES THETAIOTAOMICRON VPI
 
Authors :  K. Tan, C. Tesar, G. Cobb, A. Joachimiak, Midwest Center For Structu Genomics (Mcsg)
Date :  07 Jan 09  (Deposition) - 27 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Apc81722. 1, Methyltransferase, Bacteroides Thetaiotaomicron Vpi, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, C. Tesar, G. Cobb, A. Joachimiak
The Crystal Structure Of A Methyltransferase Domain From Bacteroides Thetaiotaomicron Vpi
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 113-224
    Gene: BACTEROIDES THETAIOTAOMICRON, BT_2273
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 818
    Strain: VPI

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:140 , ARG A:141 , GLN A:142 , THR A:143BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREGLN A:142 , LYS A:146 , GLN B:137 , SER B:160 , HIS B:162 , ARG B:163BINDING SITE FOR RESIDUE SO4 A 3
3AC3SOFTWARELYS B:139 , GLY B:140 , ARG B:141 , GLN B:142 , THR B:143BINDING SITE FOR RESIDUE SO4 B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FQ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FQ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FQ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FQ6)

(-) Exons   (0, 0)

(no "Exon" information available for 3FQ6)

(-) 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:114
 aligned with Q8A5G6_BACTN | Q8A5G6 from UniProtKB/TrEMBL  Length:224

    Alignment length:114
                                   120       130       140       150       160       170       180       190       200       210       220    
         Q8A5G6_BACTN   111 GATAFVPALVASGLPNEKFCFEGFLPQKKGRQTRLKALAEEHRTMVFYESPHRLLKTLTQFAEYFGTERQATVSREISKLHEETVRGSLAELIEHFTATEPRGEIVIVLAGIDD 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3fq6A00 A:111-224 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh......eeeee......hhhhhhhhhh....eeeeee...hhhhhhhhhhhhhh...eeeeeee.....eeeeeeehhhhhhhhhhh....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3fq6 A 111 NATAFVPALVASGLPNEKFCFEGFLPQKKGRQTRLKALAEEHRTmVFYESPHRLLKTLTQFAEYFGTERQATVSREISKLHEETVRGSLAELIEHFTATEPRGEIVIVLAGIDD 224
                                   120       130       140       150    |  160       170       180       190       200       210       220    
                                                                      155-MSE                                                                 


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with Q8A5G6_BACTN | Q8A5G6 from UniProtKB/TrEMBL  Length:224

    Alignment length:115
                                   119       129       139       149       159       169       179       189       199       209       219     
         Q8A5G6_BACTN   110 PGATAFVPALVASGLPNEKFCFEGFLPQKKGRQTRLKALAEEHRTMVFYESPHRLLKTLTQFAEYFGTERQATVSREISKLHEETVRGSLAELIEHFTATEPRGEIVIVLAGIDD 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fq6B00 B:110-224 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.....eeeeee.....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeehhhhhhhhhhh....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3fq6 B 110 SNATAFVPALVASGLPNEKFCFEGFLPQKKGRQTRLKALAEEHRTmVFYESPHRLLKTLTQFAEYFGTERQATVSREISKLHEETVRGSLAELIEHFTATEPRGEIVIVLAGIDD 224
                                   119       129       139       149     | 159       169       179       189       199       209       219     
                                                                       155-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3FQ6)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FQ6)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8A5G6_BACTN | Q8A5G6)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0070677    rRNA (cytosine-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methylcytosine.
    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:0000453    enzyme-directed rRNA 2'-O-methylation    The addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis where the methylase specifies the site that becomes methylated without using a guide RNA.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
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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