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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA/RRNA METHYLTRANSFERASE SPOU FROM RHODOBACTER SPHAEROIDES
 
Authors :  Y. Kim, C. Tesar, R. Jedrzejczak, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  30 Aug 10  (Deposition) - 08 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Alpha-Beta Sandwich, Methyltransferase, Cytosol, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, C. Tesar, R. Jedrzejczak, A. Joachimiak
Crystal Structure Of Trna/Rrna Methyltransferase Spou From Rhodobacter Sphaeroides
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRNA/RRNA METHYLTRANSFERASE (SPOU)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG29
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: RHOS4_30450, RSP_3829
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 272943
    Strain: 2.4.1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3CL1Ligand/IonCHLORIDE ION
4GOL1Ligand/IonGLYCEROL
5MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (4, 20)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2BME4Ligand/IonBETA-MERCAPTOETHANOL
3CL-1Ligand/IonCHLORIDE ION
4GOL2Ligand/IonGLYCEROL
5MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:116 , PRO A:117 , GLY A:121 , LEU A:145 , CYS A:150 , BME A:251BINDING SITE FOR RESIDUE ACY A 250
2AC2SOFTWARETHR A:81 , ALA A:82 , VAL A:136 , PHE A:143 , LEU A:145 , CYS A:150 , ACY A:250 , HOH A:301 , HOH A:324BINDING SITE FOR RESIDUE BME A 251
3AC3SOFTWAREILE A:71 , ARG A:72 , CYS A:74 , ASP A:75 , HOH A:323BINDING SITE FOR RESIDUE GOL A 252
4AC4SOFTWAREGLN A:13 , ASN A:17 , GLU A:118BINDING SITE FOR RESIDUE CL A 253
5AC5SOFTWAREVAL A:6 , ARG A:32 , ARG A:34 , ASP A:73 , CYS A:74 , ARG A:110 , VAL A:111 , GLY A:112BINDING SITE FOR RESIDUE BME A 254
6AC6SOFTWAREHIS A:60 , TYR A:76 , HOH A:287 , HOH A:296BINDING SITE FOR RESIDUE ACY A 255

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:42 -Pro A:43

 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)
  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:159
 aligned with Q3IXX1_RHOS4 | Q3IXX1 from UniProtKB/TrEMBL  Length:243

    Alignment length:159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152         
         Q3IXX1_RHOS4     3 IEPVFILVRPQMGENIGAAARAMLNFGLGRLRIVDPRDGWPNPKAVAMASGAGRLLDHAGLFPTVAEAIRDCDYVFATTARGRELTKPVMTPERAMAHGRALTGEGRRVGILFGPERTGLENEDVALANAIVTVPVNPEFFSLNLAQCVLLLAYEWRRQ 161
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -SpoU_methylase-3onpA01 A:4-156                                                                                                                           ----- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhh....eeee.......hhhhhhhhh.hhhhhhh.eee.hhhhhhh...eeeeee.........eehhhhhhhhhhhhhhh...eeeee.......hhhhhh...eeee..........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3onp A   3 IEPVFILVRPQmGENIGAAARAmLNFGLGRLRIVDPRDGWPNPKAVAmASGAGRLLDHAGLFPTVAEAIRDCDYVFATTARGRELTKPVmTPERAmAHGRALTGEGRRVGILFGPERTGLENEDVALANAIVTVPVNPEFFSLNLAQCVLLLAYEWRRQ 161
                                    12 |      22  |     32        42       |52        62        72        82        92     | 102       112       122       132       142       152         
                                      14-MSE     25-MSE                   50-MSE                                    92-MSE |                                                               
                                                                                                                          98-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 3ONP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ONP)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q3IXX1_RHOS4 | Q3IXX1)
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.
    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.
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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