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(-) Description

Title :  CRYSTAL STRUCTURE OF A RIBOSOMAL RNA METHYLTRANSFERASE, PUTATIVE, FROM PLASMODIUM FALCIPARUM (PF13_0052).
 
Authors :  A. K. Wernimont, A. Hassanali, L. Lin, J. Lew, Y. Zhao, M. Ravichandran, M. Vedadi, I. Kozieradzki, M. Schapira, A. Bochkarev, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, R. Hui, W. Qiu, Structural Consortium (Sgc)
Date :  20 Apr 07  (Deposition) - 08 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Methyltransferase, Malaria, Plasmodium Falciparum, Rna, Sam, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, A. Hassanali, L. Lin, J. Lew, Y. Zhao, M. Ravichandran G. Wasney, M. Vedadi, I. Kozieradzki, M. Schapira, A. Bochkarev, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, R. Hui, W. Qi
Crystal Structure Of A Ribosomal Rna Methyltransferase, Putative, From Plasmodium Falciparum (Pf13_0052).
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOSOMAL RNA METHYLTRANSFERASE, PUTATIVE
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15_MHL
    Expression System Strain: DH5A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 70-270
    Gene: PF13_0052
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:2 , TYR A:8 , LYS A:48 , LYS A:105 , HOH A:247 , HOH A:269 , HOH A:282 , HOH A:349BINDING SITE FOR RESIDUE SO4 A 202
2AC2SOFTWAREALA A:6 , GLY A:30 , CYS A:31 , TYR A:32 , PRO A:33 , GLY A:34 , SER A:35 , TRP A:36 , ASP A:55 , LYS A:56 , LYS A:57 , GLY A:70 , GLU A:71 , ILE A:72 , ASP A:113 , ALA A:114 , ALA A:115 , LEU A:132 , HOH A:218 , HOH A:334 , HOH A:358BINDING SITE FOR RESIDUE SAM A 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:32 -Pro A:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PLW)

(-) 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:182
 aligned with Q8IEL9_PLAF7 | Q8IEL9 from UniProtKB/TrEMBL  Length:288

    Alignment length:198
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260        
         Q8IEL9_PLAF7    71 YRSRAAYKLIELDNKYLFLKKNKIILDIGCYPGSWCQVILERTKNYKNKIIGIDKKIMDPIPNVYFIQGEIGKDNMNNIKNINYIDNMNNNSVDYKLKEILQDKKIDIILSDAAVPCIGNKIDDHLNSCELTLSITHFMEQYINIGGTYIVKMYLGSQTNNLKTYLKGMFQLVHTTKPKASRNESREIYLVCKNFLGR 268
               SCOP domains d2plwa_ A: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains FtsJ-2plwA01 A:2-196                                                                                                                                                                               --- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhh....eeeeeee..........eeee...........-----------hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee...hhhhhhhhhhh.eeeeee....-----..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2plw A   2 YRSRAAYKLIELDNKYLFLKKNKIILDIGCYPGSWCQVILERTKNYKNKIIGIDKKIMDPIPNVYFIQGEIGKDNMNNI-----------NSVDYKLKEILQDKKIDIILSDAAVPCIGNKIDDHLNSCELTLSITHFMEQYINIGGTYIVKMYLGSQTNNLKTYLKGMFQLVHTTKPK-----SREIYLVCKNFLGR 199
                                    11        21        31        41        51        61        71        |-         -|      101       111       121       131       141       151       161       171        |-    |  191        
                                                                                                         80          92                                                                                     180   186
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8IEL9_PLAF7 | Q8IEL9)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008650    rRNA (uridine-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methyluridine.
    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:0000453    enzyme-directed rRNA 2'-O-methylation    The addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis where the methylase specifies the site that becomes methylated without using a guide RNA.
    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.
cellular component
    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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