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(-) Description

Title :  CRYSTAL STRUCTURE OF PH0851
 
Authors :  Y. Hikida, M. Kuratani, Y. Bessho, R. Ishii, S. Sekine, S. Yokoyama, Rik Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Apr 07  (Deposition) - 29 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Fmu-Homolog, Methyltransferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Hikida, M. Kuratani, Y. Bessho, S. Sekine, S. Yokoyama
Structure Of An Archaeal Homologue Of The Bacterial Fmu/Rsmb/Rrmb Rrna Cytosine 5-Methyltransferase
Acta Crystallogr. , Sect. D V. 66 1301 2010
PubMed-ID: 21123870  |  Reference-DOI: 10.1107/S0907444910037558

(-) Compounds

Molecule 1 - 450AA LONG HYPOTHETICAL FMU PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0851
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: PH0851 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
1SFG1Ligand/IonSINEFUNGIN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:267 , ALA A:268 , ALA A:269 , PRO A:270 , GLY A:271 , GLY A:272 , LYS A:273 , ASP A:291 , ARG A:296 , ASP A:318 , ALA A:319 , ARG A:320 , ASP A:337 , PRO A:339 , HOH A:5761BINDING SITE FOR RESIDUE SFG A 5748

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Lys A:29 -Pro A:30
2Arg A:183 -His A:184
3Gly A:226 -Pro A:227
4Ala A:269 -Pro A:270
5Ala A:322 -Pro A:323
6Glu A:358 -Asp A:359
7Asp A:359 -Lys A:360
8Pro A:409 -Glu A:410
9Ser A:418 -Pro A:419

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YXL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YXL)

(-) Exons   (0, 0)

(no "Exon" information available for 2YXL)

(-) 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:443
 aligned with O58581_PYRHO | O58581 from UniProtKB/TrEMBL  Length:450

    Alignment length:443
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445   
         O58581_PYRHO     6 KKLSIPPKGIRAIIEAIRLGEIIKPSQYAKREAFKKHDVEEAWLNRVLTMIFYDIMKKQGLIDKVIKEIVGVTPLILDPWLRAALRVAVDIALFHDPSSQTIKNLRWKASDFISSRTHPYVGMYFWDLLDKIFEYKPNPKNELEELEWKYLAPSWLIERVKGILGDETEDFFRSVNKRHEWISIRVNTLKANVEEVIGELEEDGVEVVRSERVPTILKIKGPYNFDTSSAFNEGKIIVQEEASAVASIVLDPKPGETVVDLAAAPGGKTTHLAELMKNKGKIYAFDVDKMRMKRLKDFVKRMGIKIVKPLVKDARKAPEIIGEEVADKVLLDAPCTSSGTIGKNPELRWRLREDKINEMSQLQRELLESAARLVKPGGRLLYTTCSIFKEENEKNIRWFLNVHPEFKLVPLKSPYDPGFLEGTMRAWPHRHSTIGFFYALLEK 448
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Nol1_Nop2_Fmu-2yxlA01 A:179-447                                                                                                                                                                                                                                              - Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.....hhhhhhhhhhhh...eee......eeeee.......hhhhhh..eee.hhhhhhhhhhhh.....eeee.....hhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhh....eeee...............eeeeeee....hhhhh....hhhhhh...hhhhhhhhhhhhhhhhhh.eeeeeeeeeee...hhhhhhhhhhhhhhhh...ee.......ee......eeehhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yxl A   6 KKLSIPPKGIRAIIEAIRLGEIIKPSQYAKREAFKKHDVEEAWLNRVLTMIFYDIMKKQGLIDKVIKEIVGVTPLILDPWLRAALRVAVDIALFHDPSSQTIKNLRWKASDFISSRTHPYVGMYFWDLLDKIFEYKPNPKNELEELEWKYLAPSWLIERVKGILGDETEDFFRSVNKRHEWISIRVNTLKANVEEVIGELEEDGVEVVRSERVPTILKIKGPYNFDTSSAFNEGKIIVQEEASAVASIVLDPKPGETVVDLAAAPGGKTTHLAELMKNKGKIYAFDVDKMRMKRLKDFVKRMGIKIVKPLVKDARKAPEIIGEEVADKVLLDAPCTSSGTIGKNPELRWRLREDKINEMSQLQRELLESAARLVKPGGRLLYTTCSIFKEENEKNIRWFLNVHPEFKLVPLKSPYDPGFLEGTMRAWPHRHSTIGFFYALLEK 448
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445
   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  (0, 0)

(no "SCOP Domain" information available for 2YXL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YXL)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O58581_PYRHO | O58581)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
biological process
    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.

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  2yxl
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 Related Entries

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