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(-) Description

Title :  M. JANNASCHII NEP1
 
Authors :  A. B. Taylor, B. Meyer, B. Z. Leal, P. Kotter, P. J. Hart, K. -D. Entian, J.
Date :  09 Nov 07  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methyltransferase, Ribosome Biogenesis, S-Adenosyl-Methionine, Rrna Processing, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Taylor, B. Meyer, B. Z. Leal, P. Kotter, V. Schirf, B. Demeler, P. J. Hart, K. D. Entian, J. Wohnert
The Crystal Structure Of Nep1 Reveals An Extended Spout-Class Methyltransferase Fold And A Pre-Organized Sam-Binding Site.
Nucleic Acids Res. V. 36 1542 2008
PubMed-ID: 18208838  |  Reference-DOI: 10.1093/NAR/GKM1172

(-) Compounds

Molecule 1 - RIBOSOME BIOGENESIS PROTEIN NEP1-LIKE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NEP1
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:142 , LYS A:143 , TYR A:186 , LYS A:188 , LEU A:190BINDING SITE FOR RESIDUE GOL A 206
2AC2SOFTWAREASP A:128 , HOH A:218 , LYS B:22 , ILE B:23 , ARG B:24 , TYR B:38BINDING SITE FOR RESIDUE GOL A 207
3AC3SOFTWARETYR A:201 , SER A:202 , HOH A:320 , PRO B:150 , SER B:202BINDING SITE FOR RESIDUE GOL A 208
4AC4SOFTWARETHR A:2 , ASN A:4 , ASN A:77 , ILE A:133 , ASN A:134BINDING SITE FOR RESIDUE GOL A 209
5AC5SOFTWAREVAL A:87 , GLU A:122 , LYS A:124 , GLU A:132 , ILE A:133 , HOH A:217 , HOH A:300BINDING SITE FOR RESIDUE GOL A 210
6AC6SOFTWARETHR B:142 , LYS B:143 , TYR B:186 , LYS B:188 , GLY B:189 , LEU B:190 , VAL B:195BINDING SITE FOR RESIDUE GOL B 206
7AC7SOFTWARELYS A:136 , TYR B:79 , LYS B:89 , GLU B:122 , GLU B:132 , ILE B:133BINDING SITE FOR RESIDUE GOL B 207
8AC8SOFTWARETHR B:2 , ASN B:4 , ILE B:133 , ASN B:134BINDING SITE FOR RESIDUE GOL B 208

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BBE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BBE)

(-) 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:204
 aligned with NEP1_METJA | Q57977 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
           NEP1_METJA     2 TYNIILAKSALELIPEEIKNKIRKSRVYKYDILDSNYHYKAMEKLKDKEMRGRPDIIHISLLNILDSPINHEKKLNIYIHTYDDKVLKINPETRLPRNYFRFLGVMEKVLKGERNHLIKMEEKTLEDLLNEINAKKIAIMTKTGKLTHPKLLKEYDTFIIGGFPYGKLKINKEKVFGDIKEISIYNKGLMAWTVCGIICYSLSF 205
               SCOP domains d3bbea_ A: Ribosome biogenesis protein NEP1                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhh...........hhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhh..eeeeeee...eeeee........hhhhhhhhhhhhhh......eeeee.hhhhhhhhh...eeeee....ee.hhhhhhhh.eeeee.........hhhhh..eeeeee......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bbe A   2 TYNIILAKSALELIPEEIKNKIRKSRVYKYDILDSNYHYKAMEKLKDKEMRGRPDIIHISLLNILDSPINHEKKLNIYIHTYDDKVLKINPETRLPRNYFRFLGVMEKVLKGERNHLIKMEEKTLEDLLNEINAKKIAIMTKTGKLTHPKLLKEYDTFIIGGFPYGKLKINKEKVFGDIKEISIYNKGLMAWTVCGIICYSLSF 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with NEP1_METJA | Q57977 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
           NEP1_METJA     2 TYNIILAKSALELIPEEIKNKIRKSRVYKYDILDSNYHYKAMEKLKDKEMRGRPDIIHISLLNILDSPINHEKKLNIYIHTYDDKVLKINPETRLPRNYFRFLGVMEKVLKGERNHLIKMEEKTLEDLLNEINAKKIAIMTKTGKLTHPKLLKEYDTFIIGGFPYGKLKINKEKVFGDIKEISIYNKGLMAWTVCGIICYSLSF 205
               SCOP domains d3bbeb_ B: Ribosome biogenesis protein NEP1                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhh...........hhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhh..eeeeeee...eeeee........hhhhhhhhhhhhhh......eeeee.hhhhhhhhh...eeeee....ee.hhhhhhhh.eeeee.........hhhhh..eeeeee......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bbe B   2 TYNIILAKSALELIPEEIKNKIRKSRVYKYDILDSNYHYKAMEKLKDKEMRGRPDIIHISLLNILDSPINHEKKLNIYIHTYDDKVLKINPETRLPRNYFRFLGVMEKVLKGERNHLIKMEEKTLEDLLNEINAKKIAIMTKTGKLTHPKLLKEYDTFIIGGFPYGKLKINKEKVFGDIKEISIYNKGLMAWTVCGIICYSLSF 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BBE)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NEP1_METJA | Q57977)
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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0000462    maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)    Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript.
    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: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.
cellular component
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0032040    small-subunit processome    A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins.

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  3bbe
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  NEP1_METJA | Q57977
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 Related Entries

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

UniProtKB/Swiss-Prot
        NEP1_METJA | Q57977: 3bbd 3bbh

(-) Related Entries Specified in the PDB File

3bbd M. JANNASCHII NEP1 COMPLEXED WITH S-ADENOSYL-HOMOCYSTEINE
3bbh M. JANNASCHII NEP1 COMPLEXED WITH SINEFUNGIN