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(-) Description

Title :  THE STRUCTURE OF A PUTATIVE RNA METHYLTRANSFERASE OF THE TRMH FAMILY FROM PORPHYROMONAS GINGIVALIS.
 
Authors :  M. E. Cuff, K. E. Mussar, H. Li, S. Moy, A. Joachimiak, Midwest Center F Structural Genomics (Mcsg)
Date :  28 Aug 06  (Deposition) - 17 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Rna Methyltransferase, Trmh Family, Stuctural Genomics, Porphyromonas Gingivalis, Knot, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, K. E. Mussar, H. Li, S. Moy, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
The Structure Of A Putative Rna Methyltransferase Of The Trmh Family From Porphyromonas Gingivalis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RNA METHYLTRANSFERASE, TRMH FAMILY
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: TIGR4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SPOU, PG_0744
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619
    Strain: W83

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:107 , VAL A:108 , GLN A:109 , ASP A:110 , ASN A:113 , SER A:204 , ARG A:207 , HOH A:320 , HOH A:536BINDING SITE FOR RESIDUE ACY A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I6D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I6D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) 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)
  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:251
 aligned with Q7MW92_PORGI | Q7MW92 from UniProtKB/TrEMBL  Length:254

    Alignment length:255
                             1                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249     
         Q7MW92_PORGI     - -MLSANQIKFLRSLRERKYRLREQAFAVEGPKLVGEMLPFYRCRMLVGTAAMLRAVSTPHDAEVVELPESFDFKRISTQTTPQPLMAVFDLPAEPEPVVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEAPLPNFTEPAILVLGSEGRGISPEVAAEITDRLTIPASGLSVKGHTESLNVAIATAILCSEWRRRS 254
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i6dA01 A:0-93  [code=3.30.1330.30, no name defined]                                          2i6dA02 A:94-254  [code=3.40.1280.10, no name defined]                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.hhhhhhhhheeeeehhhhhhhhhhhh.eeeeeeehhhhhh.......eeeee....hhhhh........eeeeee...........eeeeee...hhhhhhhhhhhhhhhh..eeee........hhhhhhh..hhhhh.eeee..hhhhhhhhhhhh...eeee....ee............eeeeee......hhhhhh...eeee........----...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i6d A   0 AmLSANQIKFLRSLRERKYRLREQAFAVEGPKLVGEmLPFYRCRmLVGTAAmLRAVSTPHDAEVVELPESFDFKRISTQTTPQPLmAVFDLPAEPEPVVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASmGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEAPLPNFTEPAILVLGSEGRGISPEVAAEITDRLTIPASGLSV----ESLNVAIATAILCSEWRRRS 254
                             |       9        19        29      | 39    |   49 |      59        69        79     |  89        99       109       119       129       139       149       159       169       179       189       199       209       219       229|    | 239       249     
                             |                                 36-MSE  44-MSE 51-MSE                            85-MSE                                                        148-MSE                                                                           230  235                   
                             1-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 2I6D)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I6D)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7MW92_PORGI | Q7MW92)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008173    RNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0001510    RNA methylation    Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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