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(-) Description

Title :  THE CRYSTAL STRUCTURE OF E. COLI FMU BINARY COMPLEX WITH S-ADENOSYLMETHIONINE AT 2.1 A RESOLUTION
 
Authors :  P. G. Foster, C. R. Nunes, P. Greene, D. Moustakas, R. M. Stroud
Date :  18 Mar 04  (Deposition) - 18 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann-Fold, Mixed Beta Sheet, Methyltransferase-Fold, Rna-Binding Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. G. Foster, C. R. Nunes, P. Greene, D. Moustakas, R. M. Stroud
The First Structure Of An Rna M5C Methyltransferase, Fmu, Provides Insight Into Catalytic Mechanism And Specific Binding Of Rna Substrate
Structure V. 11 1609 2003
PubMed-ID: 14656444  |  Reference-DOI: 10.1016/J.STR.2003.10.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUN PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SUN, FMU, FMV, RSMB, B3289
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FMU PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:254 , ALA A:255 , ALA A:256 , PRO A:257 , GLY A:258 , GLY A:259 , LYS A:260 , ASP A:277 , ILE A:278 , ARG A:282 , GLY A:302 , ASP A:303 , GLY A:304 , ASP A:322 , PRO A:324 , HOH A:443 , HOH A:468 , HOH A:532BINDING SITE FOR RESIDUE SAM A 430

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:256 -Pro A:257

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_RSMB_NOPPS51686 SAM-dependent MTase RsmB/NOP-type domain profile.RSMB_ECOLI164-429  1A:164-429
2NOL1_NOP2_SUNPS01153 NOL1/NOP2/sun family signature.RSMB_ECOLI316-327  1A:316-327

(-) Exons   (0, 0)

(no "Exon" information available for 1SQF)

(-) Sequences/Alignments

Asymmetric/Biological 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:425
 aligned with RSMB_ECOLI | P36929 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:425
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424     
           RSMB_ECOLI     5 RNLRSMAAQAVEQVVEQGQSLSNILPPLQQKVSDKDKALLQELCFGVLRTLSQLDWLINKLMARPMTGKQRTVHYLIMVGLYQLLYTRIPPHAALAETVEGAIAIKRPQLKGLINGVLRQFQRQQEELLAEFNASDARYLHPSWLLKRLQKAYPEQWQSIVEANNQRPPMWLRINRTHHSRDSWLALLDEAGMKGFPHADYPDAVRLETPAPVHALPGFEDGWVTVQDASAQGCMTWLAPQNGEHILDLCAAPGGKTTHILEVAPEAQVVAVDIDEQRLSRVYDNLKRLGMKATVKQGDGRYPSQWCGEQQFDRILLDAPCSATGVIRRHPDIKWLRRDRDIPELAQLQSEILDAIWPHLKTGGTLVYATCSVLPEENSLQIKAFLQRTADAELCETGTPEQPGKQNLPGAEEGDGFFYAKLIKK 429
               SCOP domains d1sqfa1 A:5-144 Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), N-terminal domain                                     d1sqfa2 A:145-429 Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), C-terminal domain                                                                                                                                                                                     SCOP domains
               CATH domains 1sqfA01 A:5-145 N-utilizing Substance Protein B Homolog; Chain A                                                                             1sqfA02 A:146-172          1sqfA03 A:173-230 Sun protein; domain 3                   1sqfA04 A:231-429 Vaccinia Virus protein VP39                                                                                                                                                           CATH domains
               Pfam domains NusB-1sqfA02 A:5-127                                                                                                       ------------------------------------Nol1_Nop2_Fmu-1sqfA01 A:164-427                                                                                                                                                                                                                                         -- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhh..hhhhhhhhhh.....eeee.....hhhhhhhhhhhh...ee.......eeee....hhhhh.......eee.hhhhhhhhhhhh.....eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeee.....hhhhhh...eeeeeee....hhhhh....hhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee.......hhhhhhhhhhhh...ee..........eee.........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------SAM_MT_RSMB_NOP  PDB: A:164-429 UniProt: 164-429                                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NOL1_NOP2_SU------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sqf A   5 RNLRSMAAQAVEQVVEQGQSLSNILPPLQQKVSDKDKALLQELCFGVLRTLSQLDWLINKLMARPMTGKQRTVHYLIMVGLYQLLYTRIPPHAALAETVEGAIAIKRPQLKGLINGVLRQFQRQQEELLAEFNASDARYLHPSWLLKRLQKAYPEQWQSIVEANNQRPPMWLRINRTHHSRDSWLALLDEAGMKGFPHADYPDAVRLETPAPVHALPGFEDGWVTVQDASAQGCMTWLAPQNGEHILDLCAAPGGKTTHILEVAPEAQVVAVDIDEQRLSRVYDNLKRLGMKATVKQGDGRYPSQWCGEQQFDRILLDAPCSATGVIRRHPDIKWLRRDRDIPELAQLQSEILDAIWPHLKTGGTLVYATCSVLPEENSLQIKAFLQRTADAELCETGTPEQPGKQNLPGAEEGDGFFYAKLIKK 429
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: NusB] (9)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RSMB_ECOLI | P36929)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016434    rRNA (cytosine) methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methylcytosine.
    GO:0009383    rRNA (cytosine-C5-)-methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to cytosine to form 5-methylcytosine in small subunit ribosomal RNA.
    GO:0008649    rRNA methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA 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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0070475    rRNA base methylation    The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA 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.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RSMB_ECOLI | P36929: 1j4f 1sqg

(-) Related Entries Specified in the PDB File

1sqf THE CRYSTAL STRUCTURE OF THE E. COLI FMU APOENZYME AT 1.65 A RESOLUTION