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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEOGLOBUS FULGIDUS NEP1 BOUND TO S-ADENOSYLHOMOCYSTEINE
 
Authors :  S. R. Thomas, N. Laronde-Leblanc
Date :  30 Jul 10  (Deposition) - 19 Jan 11  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Spout, Ribosome Biogenesis, Methyltransferase, Rrna Processing, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Thomas, C. A. Keller, A. Szyk, J. R. Cannon, N. A. Laronde-Leblanc
Structural Insight Into The Functional Mechanism Of Nep1/Emg1 N1-Specific Pseudouridine Methyltransferase In Ribosome Biogenesis.
Nucleic Acids Res. V. 39 2445 2011
PubMed-ID: 21087996  |  Reference-DOI: 10.1093/NAR/GKQ1131

(-) Compounds

Molecule 1 - RIBOSOME BIOGENESIS NEP1 RNA METHYLTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST527
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: AF_0734
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2TYR1Mod. Amino AcidTYROSINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2TYR2Mod. Amino AcidTYROSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:153 , SER A:191 , LEU A:192 , GLY A:193 , ARG A:205BINDING SITE FOR RESIDUE TYR A 220
2AC2SOFTWAREPHE A:147 , ARG A:148 , GLU A:149 , ILE A:168 , GLY A:169 , PHE A:171 , GLY A:174 , PHE A:176 , VAL A:190 , SER A:191 , LEU A:192 , GLY A:193 , GLU A:195 , SER A:196 , TYR A:197 , SER A:199 , VAL A:202 , HOH A:238 , HOH A:320 , HOH A:383BINDING SITE FOR RESIDUE SAH A 301

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:208 -A:208

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:215 -His A:216

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O7B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O7B)

(-) Exons   (0, 0)

(no "Exon" information available for 3O7B)

(-) 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:217
 aligned with NEP1_ARCFU | O29524 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:220
                                                                                                                                                                                                                                                    219 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        |-
           NEP1_ARCFU     1 MGSAFVFLEASLELIPQKIRGHPAVRADAIRRGKRPEKILLDDSKHHTAMKSLEFREKRGRPDIVHQCLLLLLDSPLRDFEVYVHTLNGEIIWVNRETRLPRNYNRFVGLMEKLFEERRITAGDTTLIEFKDVGLRDIVRGRDVLLFREKGGRFEFSELLDGDVAVCIGAFPHGDFFEETLRELGEFKEVSLGTESYTSLYVTSRVLCEYERVRAHKVG-   -
               SCOP domains d3o7ba_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----EMG1-3o7bA01 A:5-211                                                                                                                                                                                           --------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhh.hhhhhhhhhhhh.hhhhh..hhhhhhhhh....hhhhh..hhhhhhhhhhhhh.....eeeeeee....eeee........hhhhhhhhhhhhhhhheeee..eeeeeee..hhhhhh...eeeee.......hhhhhh...eeeeee.......hhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhh.---. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o7b A   1 MGSAFVFLEASLELIPQKIRGHPAVRADAIRRGKRPEKILLDDSKHHTAMKSLEFREKRGRPDIVHQCLLLLLDSPLRDFEVYVHTLNGEIIWVNRETRLPRNYNRFVGLMEKLFEERRITAGDTTLIEFKDVGLRDIVRGRDVLLFREKGGRFEFSELLDGDVAVCIGAFPHGDFFEETLRELGEFKEVSLGTESYTSLYVTSRVLCEYERVRAH---Y 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     | 220
                                                                                                                                                                                                                                                 216 220
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O7B)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: EMG1] (5)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (NEP1_ARCFU | O29524)
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:0070037    rRNA (pseudouridine) methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a pseudouridine residue in an rRNA molecule.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    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: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:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.

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