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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF THE D/L SUBCOMPLEX OF THE SULFOLOBUS SOLFATARICUS RNA POLYMERASE
 
Authors :  A. Hirata, K. S. Murakami
Date :  27 Mar 07  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  D,L
Keywords :  Ferredoxin-Like Fe-S Binding Motif, Platform For Rna Polymerase Assembly, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hirata, B. J. Klein, K. S. Murakami
The X-Ray Crystal Structure Of Rna Polymerase From Archaea.
Nature V. 451 851 2008
PubMed-ID: 18235446  |  Reference-DOI: 10.1038/NATURE06530

(-) Compounds

Molecule 1 - DNA-DIRECTED RNA POLYMERASE SUBUNIT D
    Chains: D
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21-A
    Expression System Strain: BL21 (DE3) CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPOD
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 273057
    Strain: P2
 
Molecule 2 - DNA-DIRECTED RNA POLYMERASE SUBUNIT L
    Chains: L
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21-A
    Expression System Strain: BL21 (DE3) CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPOL
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 273057
    Strain: P2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : DL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1F3S1Ligand/IonFE3-S4 CLUSTER
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG D:29 , HIS D:153 , ALA D:154 , HOH D:3091 , HOH D:3104 , HIS L:22BINDING SITE FOR RESIDUE SO4 D 400
2AC2SOFTWARECYS D:183 , VAL D:187 , PHE D:188 , CYS D:203 , THR D:204 , LEU D:205 , CYS D:206 , GLU D:207 , GLU D:208 , CYS D:209 , ILE D:219BINDING SITE FOR RESIDUE F3S D 3076

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1D:82 -D:92
2D:85 -D:89
3D:176 -D:213

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PA8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PA8)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNA_POL_L_13KDPS01154 RNA polymerases L / 13 to 16 Kd subunits signature.RPOL_SULSO17-48  1L:17-48
2RNA_POL_D_30KDPS00446 RNA polymerases D / 30 to 40 Kd subunits signature.RPOD_SULSO26-66  1D:26-66

(-) Exons   (0, 0)

(no "Exon" information available for 2PA8)

(-) 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 D from PDB  Type:PROTEIN  Length:264
 aligned with RPOD_SULSO | P95989 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    
           RPOD_SULSO     2 SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAPNEPRMIYSKDIKSEDPSVVPISGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEILANCEKAVNVCPEGVFELKDGKLSVKNELSCTLCEECLRYCNGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKKLVEVVK 265
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...eeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeeeee....hhhhhhhhhh.......hhhhhh.hhhhh..........eeeeeeeee.....eeee.hhhee............eeeee....eeeeeeeeeee....hhhhh.eeeeeeeeeeeeee.....hhhhhh....eeee..eeee.hhhhh...hhhhhhhh..eeeeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------RNA_POL_D_30KD  PDB: D:26-66             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pa8 D   2 SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAPNEPRMIYSKDIKSEDPSVVPISGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEILANCEKAVNVCPEGVFELKDGKLSVKNELSCTLCEECLRYCNGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKKLVEVVK 265
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    


Chain L from PDB  Type:PROTEIN  Length:92
 aligned with RPOL_SULSO | Q980K0 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
           RPOL_SULSO     1 MEIRILKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLKAIENIRGMTSHYIDEIKGLTK  92
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeee..hhhhhhhhhhhhhh...eeeeeee........eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------RNA_POL_L_13KD  PDB: L:17-48    -------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2pa8 L   1 MEIRILKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLKAIENIRGMTSHYIDEIKGLTK  92
                                    10        20        30        40        50        60        70        80        90
   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 2PA8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PA8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PA8)

(-) Gene Ontology  (10, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain D   (RPOD_SULSO | P95989)
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: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: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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000428    DNA-directed RNA polymerase complex    A protein complex that possesses DNA-directed RNA polymerase activity.

Chain L   (RPOL_SULSO | Q980K0)
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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000428    DNA-directed RNA polymerase complex    A protein complex that possesses DNA-directed RNA polymerase activity.

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  2pa8
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  RPOD_SULSO | P95989
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  RPOL_SULSO | Q980K0
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPOD_SULSO | P95989: 2pmz 3hkz
        RPOL_SULSO | Q980K0: 2pmz 3hkz

(-) Related Entries Specified in the PDB File

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