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(-) Description

Title :  CRYSTAL STRUCTURE OF TANDEM WINGED HELIX DOMAIN OF RNA POLYMERASE I SUBUNIT A49 (P4)
 
Authors :  S. R. Geiger, K. Lorenzen, A. Schreieck, P. Hanecker, D. Kostrewa, A. J. P. Cramer
Date :  10 Jun 10  (Deposition) - 08 Sep 10  (Release) - 08 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Winged Helix, Transcription, Rna Polymerase, Dna Binding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. R. Geiger, K. Lorenzen, A. Schreieck, P. Hanecker, D. Kostrewa, A. J. Heck, P. Cramer
Rna Polymerase I Contains A Tfiif-Related Dna-Binding Subcomplex.
Mol. Cell V. 39 583 2010
PubMed-ID: 20797630  |  Reference-DOI: 10.1016/J.MOLCEL.2010.07.028

(-) Compounds

Molecule 1 - DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
    ChainsA, B
    EC Number2.7.7.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL 21 (DE) RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 154-399
    GeneN0880, RPA49, RRN13, YNL248C
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymA49, DNA-DIRECTED RNA POLYMERASE I 49 KDA POLYPEPTIDE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3NFH)

(-) Sites  (0, 0)

(no "Site" information available for 3NFH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NFH)

(-) 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:207
 aligned with RPA49_YEAST | Q01080 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:215
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394     
          RPA49_YEAST   185 DRPTPLANIDATDVEQIYPIESIIPKKELQFIRVSSILKEADKEKKLELFPYQNNSKYVAKKLDSLTQPSQMTKLQLLYYLSLLLGVYENRRVNNKTKLLERLNSPPEILVDGILSRFTVIKPGQFGRSKDRSYFIDPQNEDKILCYILAIIMHLDNFIVEITPLAHELNLKPSKVVSLFRVLGAIVKGATVAQAEAFGIPKSTAASYKIATMKV 399
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhh..hhhhhh..hhhhhhh.........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh....hhhhhhh.....hhhhhhhhhhh.ee..--------..ee..hhhhhhhhhhhhhhhhhh...eeehhhhhhhh...hhhhhhhhhh...eeee..hhhhhhh...hhhhhh.eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfh A 185 DRPTPLANIDATDVEQIYPIESIIPKKELQFIRVSSILKEADKEKKLELFPYQNNSKYVAKKLDSLTQPSQMTKLQLLYYLSLLLGVYENRRVNNKTKLLERLNSPPEILVDGILSRFTVIKP--------RSYFIDPQNEDKILCYILAIIMHLDNFIVEITPLAHELNLKPSKVVSLFRVLGAIVKGATVAQAEAFGIPKSTAASYKIATMKV 399
                                   194       204       214       224       234       244       254       264       274       284       294       304  |      - |     324       334       344       354       364       374       384       394     
                                                                                                                                                    307      316                                                                                   

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with RPA49_YEAST | Q01080 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:223
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396   
          RPA49_YEAST   177 QLDEITSNDRPTPLANIDATDVEQIYPIESIIPKKELQFIRVSSILKEADKEKKLELFPYQNNSKYVAKKLDSLTQPSQMTKLQLLYYLSLLLGVYENRRVNNKTKLLERLNSPPEILVDGILSRFTVIKPGQFGRSKDRSYFIDPQNEDKILCYILAIIMHLDNFIVEITPLAHELNLKPSKVVSLFRVLGAIVKGATVAQAEAFGIPKSTAASYKIATMKV 399
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) RNA_pol_I_A49-3nfhB01 B:177-399                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) RNA_pol_I_A49-3nfhB02 B:177-399                                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author ................................hhhhhhh..hhhhhh..hhhhhhh.........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh....hhhhhhh.....hhhhhhhhhhh.ee..-------...ee..hhhhhhhhhhhhhhhhhh...eeehhhhhhhh...hhhhhhhhhh...eeee..hhhhhh....hhhhhh.eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfh B 177 QLDEITSNDRPTPLANIDATDVEQIYPIESIIPKKELQFIRVSSILKEADKEKKLELFPYQNNSKYVAKKLDSLTQPSQMTKLQLLYYLSLLLGVYENRRVNNKTKLLERLNSPPEILVDGILSRFTVIKP-------DRSYFIDPQNEDKILCYILAIIMHLDNFIVEITPLAHELNLKPSKVVSLFRVLGAIVKGATVAQAEAFGIPKSTAASYKIATMKV 399
                                   186       196       206       216       226       236       246       256       266       276       286       296       306|      316       326       336       346       356       366       376       386       396   
                                                                                                                                                            307     315                                                                                    

   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  (0, 0)

(no "SCOP Domain" information available for 3NFH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RPA49_YEAST | Q01080)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0001054    RNA polymerase I activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase I specific promoter to direct initiation and catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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: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.
    GO:0006362    transcription elongation from RNA polymerase I promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I.
    GO:0006360    transcription from RNA polymerase I promoter    The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.
    GO:0042790    transcription of nuclear large rRNA transcript from RNA polymerase I promoter    The synthesis of the large ribosomal RNA (rRNA) transcript which encodes several rRNAs, e.g. in mammals 28S, 18S and 5.8S, from a nuclear DNA template transcribed by RNA polymerase I.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005736    DNA-directed RNA polymerase I complex    RNA polymerase I, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces rRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase III and others of which are also found in RNA polymerases II and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RPA49_YEAST | Q010803nfi 4c2m 4c3h 4c3i 4c3j 4ym7 5g5l 5lmx 5m3f 5m3m 5m5w 5m5x 5m5y 5m64 5n5y 5n5z 5n60 5n61

(-) Related Entries Specified in the PDB File

3nff 3nfg 3nfi