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(-) Description

Title :  PUTATIVE TETRAPYRROLE (CORRIN/PORPHYRIN) METHYLTRANSFERASE FROM BACTEROIDES FRAGILIS.
 
Authors :  J. Osipiuk, L. Volkart, G. Cobb, Y. Kim, A. Joachimiak, Midwest Center Structural Genomics (Mcsg)
Date :  04 Dec 08  (Deposition) - 16 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Apc62130. 1, Methyltransferase, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, L. Volkart, G. Cobb, Y. Kim, A. Joachimiak
X-Ray Crystal Structure Of Putative Tetrapyrrole (Corrin/Porphyrin) Methyltransferase From Bacteroides Fragilis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE TETRAPYRROLE (CORRIN/PORPHYRIN) METHYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BF0585
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 272559
    Strain: NCTC 9343

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:138 , LYS A:139 , GLY A:140 , ARG A:141 , MSE A:142 , THR A:143BINDING SITE FOR RESIDUE SO4 A 225
2AC2SOFTWAREHOH A:23 , SER A:188 , HIS A:205BINDING SITE FOR RESIDUE SO4 A 226

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:112
 aligned with Q5LHP3_BACFN | Q5LHP3 from UniProtKB/TrEMBL  Length:224

    Alignment length:112
                                   120       130       140       150       160       170       180       190       200       210       220  
         Q5LHP3_BACFN   111 GATAFVPALVASGLPNEKFCFEGFLPQKKGRMTKLKSLVDEHRTMVFYESPHRLLKTLTQFAEYFGPERQVSVSREISKIHEETVRGTLSELIEHFTATDPRGEIVIVLAGI 222
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ffyA00 A:111-222 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh......eeeee......hhhhhhhhh.....eeeeee...hhhhhhhhhhhhhh...eeeeeee.....eeeeeeehhhhhhhhhhh.....eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3ffy A 111 NATAFVPALVASGLPNEKFCFEGFLPQKKGRmTKLKSLVDEHRTmVFYESPHRLLKTLTQFAEYFGPERQVSVSREISKIHEETVRGTLSELIEHFTATDPRGEIVIVLAGI 222
                                   120       130       140 |     150    |  160       170       180       190       200       210       220  
                                                         142-MSE      155-MSE
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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  (0, 0)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5LHP3_BACFN | Q5LHP3)
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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