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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CONSERVED HYPOTHETICAL PROTEIN, METHYLTRANSFERASE FROM STREPTOCOCCUS PNEUMONIAE TIGR4
 
Authors :  Midwest Center For Structural Genomics (Mcsg)
Date :  28 Feb 05  (Deposition) - 12 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Methyltransferase, Alpha-Beta-Alpha Sandwich, S-Adenosylmethionine- Dependent, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, H. Li, F. Collart, A. Joachimiak
Crystal Structure Of The Conserved Methyltransferase From Streptococcus Pneumoniae Tigr4
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID WITH T7 PROMOTER
    Gene: TRMB, SP0550
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Synonym: TRNA(M7G46)-METHYLTRANSFERASE

 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, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:110 , ARG B:111 , GLU B:148BINDING SITE FOR RESIDUE GOL B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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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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  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:204
 aligned with TRMB_STRPN | P67506 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:204
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207    
           TRMB_STRPN     8 GATELLEANPQYVVLNPLEAKAKWRDLFGNDNPIHVEVGSGKGAFVSGMAKQNPDINYIGIDIQKSVLSYALDKVLEVGVPNIKLLWVDGSDLTDYFEDGEIDRLYLNFSDPWPKKRHEKRRLTYKTFLDTFKRILPENGEIHFKTDNRGLFEYSLVSFSQYGMKLNGVWLDLHASDFEGNVMTEYEQKFSNKGQVIYRVEAEF 211
               SCOP domains d1yzha1 A:8-211 tRNA (guanine-N(7)-)-methyltransferase TrmB                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh....ee.hhhhh..hhhhhhh....eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeee....hhhhh.......eeeee......hhhhhhhh..hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yzh A   8 GATELLEANPQYVVLNPLEAKAKWRDLFGNDNPIHVEVGSGKGAFVSGmAKQNPDINYIGIDIQKSVLSYALDKVLEVGVPNIKLLWVDGSDLTDYFEDGEIDRLYLNFSDPWPKKRHEKRRLTYKTFLDTFKRILPENGEIHFKTDNRGLFEYSLVSFSQYGmKLNGVWLDLHASDFEGNVmTEYEQKFSNKGQVIYRVEAEF 211
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167   |   177       187  |    197       207    
                                                                           56-MSE                                                                                                            171-MSE            190-MSE                 


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with TRMB_STRPN | P67506 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:206
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      
           TRMB_STRPN     6 RKGATELLEANPQYVVLNPLEAKAKWRDLFGNDNPIHVEVGSGKGAFVSGMAKQNPDINYIGIDIQKSVLSYALDKVLEVGVPNIKLLWVDGSDLTDYFEDGEIDRLYLNFSDPWPKKRHEKRRLTYKTFLDTFKRILPENGEIHFKTDNRGLFEYSLVSFSQYGMKLNGVWLDLHASDFEGNVMTEYEQKFSNKGQVIYRVEAEF 211
               SCOP domains d1yzhb_ B: tRNA (guanine-N(7)-)-methyltransferase TrmB                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh....ee........hhhhhhh....eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeee....hhhhh.......eeeee......hhhhhhhh..hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhh......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yzh B   6 RKGATELLEANPQYVVLNPLEAKAKWRDLFGNDNPIHVEVGSGKGAFVSGmAKQNPDINYIGIDIQKSVLSYALDKVLEVGVPNIKLLWVDGSDLTDYFEDGEIDRLYLNFSDPWPKKRHEKRRLTYKTFLDTFKRILPENGEIHFKTDNRGLFEYSLVSFSQYGmKLNGVWLDLHASDFEGNVmTEYEQKFSNKGQVIYRVEAEF 211
                                    15        25        35        45        55|       65        75        85        95       105       115       125       135       145       155       165     | 175       185    |  195       205      
                                                                             56-MSE                                                                                                            171-MSE            190-MSE
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 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YZH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRMB_STRPN | P67506)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008176    tRNA (guanine-N7-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N7-methylguanine.
    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:0036265    RNA (guanine-N7)-methylation    The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an RNA molecule.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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