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(-) Description

Title :  T7 RNA POLYMERASE ALPHA BETA METHYLENE ATP ELONGATION COMPLEX
 
Authors :  Y. W. Yin, T. A. Steitz
Date :  29 Jan 04  (Deposition) - 23 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.88
Chains :  Asym./Biol. Unit :  D,N,R,T
Keywords :  T7 Rna Polymerase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. W. Yin, T. A. Steitz
The Structural Mechanism Of Translocation And Helicase Activity In T7 Rna Polymerase.
Cell(Cambridge, Mass. ) V. 116 393 2004
PubMed-ID: 15016374  |  Reference-DOI: 10.1016/S0092-8674(04)00120-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(P*GP*CP*CP*GP*TP*GP*CP*GP*CP*AP*TP*TP*CP*GP*CP*CP*GP*TP*G P*TP*T)-3')
    Chains: T
    Engineered: YES
    Other Details: DNA OLIGOMER IS SYNTHESIZED
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(P*TP*TP*TP*AP*CP*GP*TP*TP*GP*CP*GP*CP*AP*CP*GP*GP*C)-3')
    Chains: N
    Engineered: YES
    Other Details: DNA OLIGOMER IS SYNTHESIZED
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(P*AP*CP*AP*CP*GP*GP*CP*GP*A)-3')
    Chains: R
    Engineered: YES
    Other Details: RNA OLIGOMER IS SYNTHESIZED
    Synthetic: YES
 
Molecule 4 - DNA-DIRECTED RNA POLYMERASE
    Chains: D
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ENTEROBACTERIA PHAGE T7
    Organism Taxid: 10760

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : DNRT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP D:537 , GLY D:538 , ASP D:812 , MG D:903 , APC R:901BINDING SITE FOR RESIDUE MG D 902
2AC2SOFTWAREASP D:537 , ASP D:812 , MG D:902 , A R:2 , APC R:901BINDING SITE FOR RESIDUE MG D 903
3AC3SOFTWAREASP D:537 , GLY D:538 , CYS D:540 , SER D:541 , TYR D:571 , ARG D:627 , LYS D:631 , TYR D:639 , HIS D:784 , ASP D:812 , MG D:902 , MG D:903 , A R:2 , DT T:119 , DT T:120BINDING SITE FOR RESIDUE APC R 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S76)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S76)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S76)

(-) 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  1D:533-544
2RNA_POL_PHAGE_2PS00489 Bacteriophage-type RNA polymerase family active site signature 2.RPOL_BPT7625-639  1D:625-639

(-) Exons   (0, 0)

(no "Exon" information available for 1S76)

(-) 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:829
 aligned with RPOL_BPT7 | P00573 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:872
                                    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       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881  
            RPOL_BPT7    12 SDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
               SCOP domains d1s76d_ D: T7 RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1s76D01 D:12-325 T7 RNA polymerase, domain 1                                                                                                                                                                                                                                                                              1s76D02 D:326-411  [code=1.10.287.260            , no name defined]                   ---------1s76D03                      1s76D04 D:450-527  [code=1.10.287.280, no name defined]                       1s76D03                   1s76D05 D:554-784 5' to 3' exonuclease,                   C-terminal subdomain                                                                                                                                                         1s76D03 D:421-449,D:528-553,D:785-872  [code=3.30.70.370, no name defined]              ----------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------     ---------------------------------        --------------------------------------------------------------------------------------------------------------------------            --------------------------------------------------------------------------RNA_pol-1s76D01 D:449-883                                                                                                                                                                                                                                                                                                                                                                                                                           Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..................hhhhhh.....hhhhhhhhhhhhh.....-----....hhhhhhhhhhhhhhhhhh.....eee...--------...eee....hhhhhhhhhhhhh.....................................hhhhhhh.....hhhhhhhhhhhhh..eeehhhhhhhhhhhh....................------------.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh........eee.....eee........hhhhhhheee...eehhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhh...ee...eeee..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.........------------------..hhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh................eeee.....eeee.........ee.....ee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_POL_PHAG--------------------------------------------------------------------------------RNA_POL_PHAGE_2---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s76 D  12 SDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKG-----AWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQ--------SETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPM------------TAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNE------------------GTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
                                    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       271       281       291       301       311       321       331       341       351       361|        -   |   381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591 |       -         -|      621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881  
                                                                                                                                                                                                                194   200                             232      241                                                                                                                      362          375                                                                                                                                                                                                                       593                612                                                                                                                                                                                                                                                                               


Chain N from PDB  Type:DNA  Length:17
                                                 
                 1s76 N  14 TTTACGTTGCGCACGGC  30
                                    23       


Chain R from PDB  Type:RNA  Length:9
                                         
                 1s76 R  10 ACACGGCGA   2
                            |||||||||
                           10||||||||
                             9|||||||
                              8||||||
                               7|||||
                                6||||
                                 5|||
                                  4||
                                   3|
                                    2


Chain T from PDB  Type:DNA  Length:21
                                                     
                 1s76 T 130 GCCGTGCGCATTCGCCGTGTT 110
                            |||||||121|||||||111|
                            ||||||122||||||113|||
                          130||||||121||||||112||
                           129||||||120||||||111|
                            128||||| 119||||| 110
                             127||||  118||||    
                              126|||   117|||    
                               125||    116||    
                                124|     115|    
                                 123      114
   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 D   (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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  1s76
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  RPOL_BPT7 | P00573
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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 1qln 1s0v 1s77 2pi4 2pi5 3e2e 3e3j 4rnp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1S76)