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(-) Description

Title :  CRYSTAL STRUCTURE OF P23-45 GP39 (6-109) BOUND TO THERMUS THERMOPHILUS RNA POLYMERASE BETA-FLAP DOMAIN
 
Authors :  S. Tagami, S. Sekine, L. Minakhin, D. Esyunina, R. Akasaka, M. Shirouzu A. Kulbachinskiy, K. Severinov, S. Yokoyama
Date :  26 Dec 13  (Deposition) - 12 Mar 14  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transcription, Rna Polymerase, Transferase-Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Tagami, S. Sekine, L. Minakhin, D. Esyunina, R. Akasaka, M. Shirouzu, A. Kulbachinskiy, K. Severinov, S. Yokoyama
Structural Basis For Promoter Specificity Switching Of Rna Polymerase By A Phage Factor.
Genes Dev. V. 28 521 2014
PubMed-ID: 24589779  |  Reference-DOI: 10.1101/GAD.233916.113

(-) Compounds

Molecule 1 - DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA
    Chains: A, C
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 703-830
    Gene: RPOB, TTHA1813
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: RNAP SUBUNIT BETA, RNA POLYMERASE SUBUNIT BETA, TRANSCRIPTASE SUBUNIT BETA
 
Molecule 2 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-47B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 4-109
    Gene: GP39 (P23P39), P23P39
    Organism Scientific: THERMUS PHAGE P23-45
    Organism Taxid: 466051
    Strain: THERMUS PHAGE P23-45
    Synonym: GP39

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3WOE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WOE)

(-) 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:130
 aligned with RPOB_THET8 | Q8RQE9 from UniProtKB/Swiss-Prot  Length:1119

    Alignment length:173
                                   667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827   
           RPOB_THET8   658 GPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQK 830
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-------------------------------------------eeeeeeeeeee.......ee.......hhhhhh............ee....eee.eeee......hhhhhhhhhhhh.....eee..ee......eeeeeeeeee...........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3woe A 701 GP-------------------------------------------IHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQK 830
                             |       -         -         -         -     | 707       717       727       737       747       757       767       777       787       797       807       817       827   
                           702                                         703                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:104
 aligned with A7XX65_9CAUD | A7XX65 from UniProtKB/TrEMBL  Length:141

    Alignment length:104
                                    15        25        35        45        55        65        75        85        95       105    
         A7XX65_9CAUD     6 VEPYIRLFEAIPDAETELATFYDADLDTLPPRMFLPSGDLYTPPGPVRLEEIKRKRRVRLVKVSIYRFEHVGLGLAARPYAYAYAWQGDNGILHLYHAPVVLED 109
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh......................ee.....ee.....eeeeeeee....eeeeeeeeeeeee..eeeeeeeeeeeeee.....eee....ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3woe B   6 VEPYIRLFEAIPDAETELATFYDADLDTLPPRmFLPSGDLYTPPGPVRLEEIKRKRRVRLVKVSIYRFEHVGLGLAARPYAYAYAWQGDNGILHLYHAPVVLED 109
                                    15        25        35  |     45        55        65        75        85        95       105    
                                                           38-MSE                                                                   


Chain C from PDB  Type:PROTEIN  Length:130
 aligned with RPOB_THET8 | Q8RQE9 from UniProtKB/Swiss-Prot  Length:1119

    Alignment length:173
                                   667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827   
           RPOB_THET8   658 GPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQK 830
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-------------------------------------------..eeeeeeeee.......ee.......hhhhhh............ee....eee.eeee......hhhhhhhhhhhh.....eee..ee......eeeeeeeeee...........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3woe C 701 GP-------------------------------------------IHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQK 830
                             |       -         -         -         -     | 707       717       727       737       747       757       767       777       787       797       807       817       827   
                           702                                         703                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:104
 aligned with A7XX65_9CAUD | A7XX65 from UniProtKB/TrEMBL  Length:141

    Alignment length:104
                                    15        25        35        45        55        65        75        85        95       105    
         A7XX65_9CAUD     6 VEPYIRLFEAIPDAETELATFYDADLDTLPPRMFLPSGDLYTPPGPVRLEEIKRKRRVRLVKVSIYRFEHVGLGLAARPYAYAYAWQGDNGILHLYHAPVVLED 109
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh......................ee.....ee.....eeeeeeee....eeeeeeeeeeee....eeeeeeeeeeeee.....eee....ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3woe D   6 VEPYIRLFEAIPDAETELATFYDADLDTLPPRmFLPSGDLYTPPGPVRLEEIKRKRRVRLVKVSIYRFEHVGLGLAARPYAYAYAWQGDNGILHLYHAPVVLED 109
                                    15        25        35  |     45        55        65        75        85        95       105    
                                                           38-MSE
   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 3WOE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (RPOB_THET8 | Q8RQE9)
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:0032549    ribonucleoside binding    Interacting selectively and non-covalently with a ribonucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked to ribose.
    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.

Chain B,D   (A7XX65_9CAUD | A7XX65)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RPOB_THET8 | Q8RQE9: 1iw7 1smy 1zyr 2a68 2a69 2a6e 2a6h 2be5 2cw0 2o5i 2o5j 2ppb 3aoh 3aoi 3dxj 3eql 3wod 3wof 4g7h 4g7o 4g7z 4gzy 4gzz 4mq9 4oin 4oio 4oip 4oiq 4oir 4q4z 4q5s 4wqs 4wqt 5d4c 5d4d 5d4e 5e17 5e18 5i2d 5tmc 5tmf 5vo8 5voi 5x21 5x22
UniProtKB/TrEMBL
        A7XX65_9CAUD | A7XX65: 3wod 3wof

(-) Related Entries Specified in the PDB File

3wod 3wof