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(-) Description

Title :  STRUCTURE OF A TRANSCRIBING T7 RNA POLYMERASE INITIATION COMPLEX
 
Authors :  G. M. T. Cheetham, T. A. Steitz
Date :  01 Sep 99  (Deposition) - 04 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,N,R,T
Keywords :  Nucleotidyltransferase, T7 Rna Polymerase, Protein/Dna/Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. M. T. Cheetham, T. A. Steitz
Structure Of A Transcribing T7 Rna Polymerase Initiation Complex
Science V. 286 2305 1999
PubMed-ID: 10600732  |  Reference-DOI: 10.1126/SCIENCE.286.5448.2305

(-) Compounds

Molecule 1 - BACTERIOPHAGE T7 RNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAR1219
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: BACTERIOPHAGE T7
    Organism Taxid: 10760
 
Molecule 2 - DNA (5- D (P*CP*TP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP* AP*TP*TP*A)-3)
    Chains: T
    Fragment: PROMOTER
    Organism Scientific: BACTERIOPHAGE T7
    Organism Taxid: 10760
    Synonym: TEMPLATE STRAND
    Synthetic: YES
 
Molecule 3 - DNA (5- D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)-3)
    Chains: N
    Fragment: PROMOTER
    Organism Scientific: BACTERIOPHAGE T7
    Organism Taxid: 10760
    Synonym: NON-TEMPLATE STRAND
    Synthetic: YES
 
Molecule 4 - RNA (5- R(PPP*GP*GP*G)-3)
    Chains: R
    Fragment: TRANSCRIPT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ANRT

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1QLN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QLN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QLN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QLN)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNA_POL_PHAGE_1PS00900 Bacteriophage-type RNA polymerase family active site signature 1.RPOL_BPT7533-544  1A:533-544
2RNA_POL_PHAGE_2PS00489 Bacteriophage-type RNA polymerase family active site signature 2.RPOL_BPT7625-639  1A:625-639

(-) Exons   (0, 0)

(no "Exon" information available for 1QLN)

(-) 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:862
 aligned with RPOL_BPT7 | P00573 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:878
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875        
            RPOL_BPT7     6 IAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
               SCOP domains d1qlna_ A: T7 RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --1qlnA01 A:8-325 T7 RNA polymerase, domain 1                                                                                                                                                                                                                                                                                   1qlnA02 A:326-411  [code=1.10.287.260, no name defined]                               ---------1qlnA03                      1qlnA04 A:450-527  [code=1.10.287.280, no name defined]                       1qlnA03                   1qlnA05 A:554-784 5' to 3' exonuclease, C-terminal subdomain                                                                                                                                                                           1qlnA03 A:421-449,A:528-553,A:785-872  [code=3.30.70.370, no name defined]              ----------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_pol-1qlnA01 A:449-883                                                                                                                                                                                                                                                                                                                                                                                                                           Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhh.----------------.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh............hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..eeeeee........eeeeeehhhhhhhhhhh...........................................hhhhhhh.....hhhhhhhhhhhhh..eeehhhhhhhhhhhh.............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee.....eee........hhhhhhheee.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhh.hhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeee.....eeee......eee..eee...eee..eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_POL_PHAG--------------------------------------------------------------------------------RNA_POL_PHAGE_2---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qln A   6 IAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMF----------------PLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
                                    15        25        35        45        55         -      | 75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875        
                                                                            55               72                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           


Chain N from PDB  Type:DNA  Length:14
                                              
                 1qln N 101 TAATACGACTCACT 114
                                   110    


Chain R from PDB  Type:RNA  Length:3
                                   
                 1qln R   1 gGG   3
                            |  
                            1-GTP


Chain T from PDB  Type:DNA  Length:22
                                                      
                 1qln T   1 CTCCCTATAGTGAGTCGTATTA  22
                                    10        20
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (5, 5)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RNA_pol] (7)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RPOL_BPT7 | P00573)
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: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:0039695    DNA-templated viral transcription    A transcription process that uses a viral DNA as a template.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  1qln
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  2.7.7.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPOL_BPT7 | P00573: 1aro 1cez 1h38 1msw 1s0v 1s76 1s77 2pi4 2pi5 3e2e 3e3j 4rnp

(-) Related Entries Specified in the PDB File

1aro T7 RNA POLYMERASE COMPLEXED WITH T7 LYSOZYME
1cez CRYSTAL STRUCTURE OF A T7 RNA POLYMERASE-T7 PROMOTER COMPLEX
4rnp BACTERIOPHAGE T7 RNA POLYMERASE, HIGH SALT CRYSTAL FORM, LOW TEMPERATURE DATA, ALPHA-CARBONS ONLY