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(-) Description

Title :  TAQ RNA POLYMERASE-RIFAMPICIN COMPLEX
 
Authors :  E. A. Campbell, O. Pavlova, N. Zenkin, F. Leon, H. Irschik, R. Jansen, K. Severinov, S. A. Darst
Date :  24 Jan 05  (Deposition) - 15 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C,D,J,K
Keywords :  Transferase, Rna Polymerase, Rifampicin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Campbell, O. Pavlova, N. Zenkin, F. Leon, H. Irschik, R. Jansen, K. Severinov, S. A. Darst
Structural, Functional, And Genetic Analysis Of Sorangicin Inhibition Of Bacterial Rna Polymerase
Embo J. V. 24 674 2005
PubMed-ID: 15692574  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600499
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA-DIRECTED RNA POLYMERASE ALPHA CHAIN
    Chains: A, B
    EC Number: 2.7.7.6
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: RNAP ALPHA SUBUNIT, TRANSCRIPTASE ALPHA CHAIN, RNA POLYMERASE ALPHA SUBUNIT
 
Molecule 2 - DNA-DIRECTED RNA POLYMERASE BETA CHAIN
    Chains: C
    EC Number: 2.7.7.6
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: RNAP BETA SUBUNIT, TRANSCRIPTASE BETA CHAIN, RNA POLYMERASE BETA SUBUNIT
 
Molecule 3 - DNA-DIRECTED RNA POLYMERASE BETA' CHAIN
    Chains: D, J
    EC Number: 2.7.7.6
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: RNAP BETA' SUBUNIT, TRANSCRIPTASE BETA' CHAIN, RNA POLYMERASE BETA' SUBUNIT
 
Molecule 4 - DNA-DIRECTED RNA POLYMERASE OMEGA CHAIN
    Chains: K
    EC Number: 2.7.7.6
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: RNAP OMEGA SUBUNIT, TRANSCRIPTASE OMEGA CHAIN, RNA POLYMERASE OMEGA SUBUNIT

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDJK

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1RFP1Ligand/IonRIFAMPICIN
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS D:58 , ALA D:59 , CYS D:60 , CYS D:76BINDING SITE FOR RESIDUE ZN D 1525
2AC2SOFTWARECYS D:1112 , CYS D:1194 , CYS D:1201 , CYS D:1204BINDING SITE FOR RESIDUE ZN D 1526
3AC3SOFTWAREGLN C:390 , SER C:392 , GLN C:393 , PHE C:394 , ASP C:396 , ARG C:405 , HIS C:406 , ARG C:409 , SER C:411 , ILE C:452BINDING SITE FOR RESIDUE RFP C 1120

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNA_POL_BETAPS01166 RNA polymerases beta chain signature.RPOB_THEAQ836-848  1C:836-848

(-) Exons   (0, 0)

(no "Exon" information available for 1YNN)

(-) 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:230
 aligned with RPOA_THEAQ | Q9KWU8 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:230
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235
          RPOA_THEAQ      6 LKAPVFTATTQGDHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEGGKLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPT  235
               SCOP domains d1ynna1 A:6-49,A:173-231                    d1ynna2 A:50-172 RNA polymerase alpha subunit                                                                              d1ynna1 A:6-49,A:173-231 RNA polymerase alpha              ---- SCOP domains
               CATH domains 1ynnA01 A:6-49,A:172-225                    1ynnA02 A:50-171 RNA Polymerase Alpha Subunit; Chain A, domain 2                                                          1ynnA01 A:6-49,A:172-225                              ---------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhh.eee.....................hhhhhhhhhh...ee.......eeeeee.....ee............ee........ee.......eeeeeeee..eehhhhhh...........ee........eeeee.........eeeee........hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ynn A    6 LKAPVFTATTQGDHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEGGKLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPT  235
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with RPOA_THEAQ | Q9KWU8 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
          RPOA_THEAQ      4 SKLKAPVFTATTQGDHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEGGKLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVAILKEHLNYFANP  228
               SCOP domains --d1ynnb1 B:6-49,B:173-228                    d1ynnb2 B:50-172 RNA polymerase alpha subunit                                                                              d1ynnb1 B:6-49,B:173-228 RNA polymerase alpha            SCOP domains
               CATH domains 1ynnB01 B:4-49,B:172-225                      1ynnB02 B:50-171 RNA Polymerase Alpha Subunit; Chain A, domain 2                                                          1ynnB01 B:4-49,B:172-225                              --- CATH domains
           Pfam domains (1) ---------------------RNA_pol_L-1ynnB01 B:25-223                                                                                                                                                                             ----- Pfam domains (1)
           Pfam domains (2) ---------------------RNA_pol_L-1ynnB02 B:25-223                                                                                                                                                                             ----- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------RNA_pol_A_bac-1ynnB03 B:52-179                                                                                                  ------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------RNA_pol_A_bac-1ynnB04 B:52-179                                                                                                  ------------------------------------------------- Pfam domains (4)
         Sec.struct. author .......ee........eeeeeeee..hhhhhhhhhhhhhhh....eeeeeeeee...............hhhhhhhhhhh..eee......eeeeeee....eeehhhhh.....eee.......eee......eeeeeeeee....hhhhhh......eee.......eeeeeeeeeeeee..eeeeeeeeeeeee....hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ynn B    4 SKLKAPVFTATTQGDHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEGGKLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVAILKEHLNYFANP  228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     


Chain C from PDB  Type:PROTEIN  Length:1114
 aligned with RPOB_THEAQ | Q9KWU7 from UniProtKB/Swiss-Prot  Length:1119

    Alignment length:1114
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110    
          RPOB_THEAQ      1 MEIKRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIRTPYRRVKNGVVTEEVVYMTASEEDRYTIAQANTPLEGDRIATDRVVARRRGEPVIVAPEEVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVVKVDGTRIAVRYEDGRLVEHPLRRYARSNQGTAFDQRPRVRVGQRVKKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEG 1114
               SCOP domains d1ynnc1 C:1-1114 RNA-polymerase beta                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1ynnC01 1ynnC02 C:9-143,C:325-469,C:536-592  [code=3.90.1100.10, no name defined]                                                              1ynnC03 C:144-324  [code=3.90.1110.10, no name defined]                                                                                                                              1ynnC02 C:9-143,C:325-469,C:536-592  [code=3.90.1100.10, no name defined]                                                                        1ynnC04 C:470-535  [code=2.30.150.10, no name defined]            1ynnC02 C:9-143,C:325-469,C:536-592                      1ynnC05 C:593-667  [code=2.40.50.100, no name defined]                     1ynnC01 C:1-8,C:668-702,C:831-1004 1ynnC06 C:703-830  [code=2.40.50.150, no name defined]                                                                          1ynnC01 C:1-8,C:668-702,C:831-1004  [code=2.40.270.10, no name defined]                                                                                                       -------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------RNA_pol_Rpb2_1-1ynnC02 C:17-389                                                                                                                                                                                                                                                                                                                                                      ---RNA_pol_Rpb2_3-1ynnC04 C:393-462                                      --------RNA_pol_Rpb2_45-1ynnC05 C:471-535                                -----RNA_pol_Rpb2_6-1ynnC01 C:541-1026                                                                                                                                                                                                                                                                                                                                                                                                                                                                     -RNA_pol_Rpb2_7-1ynnC06 C:1028-1104                                           ---------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------RNA_pol_Rpb2_2-1ynnC03 C:142-334                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..eee.............hhhhhhhhhhhhh...........hhhhhhhhhh..............eeeeeee.....hhhhhhhh....eeeeeeeee.............eeeeeee.......ee....eeee.eeeee..ee............eeeee........eeee........eee..eeehhhhhhhhh....hhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhh..............hhhhhhhhhhh.........eee....ee..hhhhhhhhhhh..................eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh..ee.....hhhhhhhhhheee........................................eee.....ee.....eeeeeee.........eeee.........ee.....ee..ee....eeee....eeee......eee.hhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh..........ee..hhhhhhhhh...ee....eeeeee...eeeeee....eeeee...............ee............eeee...ee..ee...eeeeeee...........eeeehhhhhh.....eeeeeeeeeeeee..ee..........hhhhhh............ee......................hhhhhhh...................eeeeeeeee............eeeeeeeeeeee........ee........eeeee...............eeehhhhh.....hhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhhhhhhhhh.ee..............eeeeeeeeee....................................hhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhhhhhhhhhh.....eee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_POL_BETA -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ynn C    1 MEIKRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIRTPYRRVKNGVVTEEVVYMTASEEDRYTIAQANTPLEGDRIATDRVVARRRGEPVIVAPEEVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVVKVDGTRIAVRYEDGRLVEHPLRRYARSNQGTAFDQRPRVRVGQRVKKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEG 1114
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110    


Chain D from PDB  Type:PROTEIN  Length:1238
 aligned with RPOC_THEAQ | Q9KWU6 from UniProtKB/Swiss-Prot  Length:1524

    Alignment length:1238
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232        
          RPOC_THEAQ      3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFNKYIVLDPKGAVLDGVPVEKRQLLTDEEYRELRYGKQETYPLPAGVDALVKDGEEVVKGQELAPGVVSRMDGVALYRFPRRVRVDYLRKERAALRIPLSAWVEKEAYRPGEVLAELSEPYLFRAEESGVVELKDLAEGHLIYLRQEEEVVARYFLPAGMTPLVVEGEIVEVGQPLAEGKGLLRLPRHMTAKEVEAEEEGDSVHLTLFLEWTEPKDYKVAPHMNVIVPEGAKVQAGEKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVTTGDRVAPGDVLADGGKVKSEIYGRVEVDLVRNVVRVVESYDIDARMGAEAIQELLKELDLEKLERELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADCGTTNYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRT 1240
               SCOP domains d1ynnd1 D:3-1240 RNA-polymerase beta-prime                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_pol_Rpb1_1-1ynnD01 D:417-618                                                                                                                                                                          -RNA_pol_Rpb1_2-1ynnD03 D:620-765                                                                                                                  --RNA_pol_Rpb1_3-1ynnD04 D:768-954                                                                                                                                                           ----------------------------RNA_pol_Rpb1_4-1ynnD05 D:983-1066                                                   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_pol_Rpb1_1-1ynnD02 D:417-618                                                                                                                                                                          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eee....hhhhhhhhh............................................................hhhhh...eeee......hhhhhh...............hhhhhh.....ee.................eehhhhhhhhh...eeeee.............ee...............ee..eeeeee..eeee.....eeeee.hhh............ee....eeee....eeeeeeee..eeeeeeee..eeeeeeee...eee......ee....eeeee..ee...........eeeee..eeeee.....eee.........ee............eeee.......ee....eee..eeeeeeeee.eeeee...........ee...ee.......ee...eeeeee....eeeeee.......hhhhhhhhhhhh.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.........eeee.hhhhh..ee.....ee..hhhhhhhhhhhhhhh.hhhhhh.........hhhhhhhhhhhhhhh...........................hhhhhhhhh.....eeeeeeee.......ee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhh...eeeee....hhh.eeeeee.......eee...hhhhhh......eeeee...hhhhhhhhhhhhhhhhh...............hhhhhhhhh...................hhhhhhh................hhhhh..ee.hhhhhhhhhhh.........eee....ee..hhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhh...eeee.....eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..............eeee.eeee....eeee.hhhhhhhhhh.ee....eee..eee....eehhhhhhhhhhhhhh....eeee.hhhhh.........................hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ynn D    3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFNKYIVLDPKGAVLDGVPVEKRQLLTDEEYRELRYGKQETYPLPAGVDALVKDGEEVVKGQELAPGVVSRMDGVALYRFPRRVRVDYLRKERAALRIPLSAWVEKEAYRPGEVLAELSEPYLFRAEESGVVELKDLAEGHLIYLRQEEEVVARYFLPAGMTPLVVEGEIVEVGQPLAEGKGLLRLPRHMTAKEVEAEEEGDSVHLTLFLEWTEPKDYKVAPHMNVIVPEGAKVQAGEKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVTTGDRVAPGDVLADGGKVKSEIYGRVEVDLVRNVVRVVESYDIDARMGAEAIQELLKELDLEKLERELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADCGTTNYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRT 1240
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232        


Chain J from PDB  Type:PROTEIN  Length:249
 aligned with RPOC_THEAQ | Q9KWU6 from UniProtKB/Swiss-Prot  Length:1524

    Alignment length:249
                                  1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412      1422      1432      1442      1452      1462      1472      1482      1492         
          RPOC_THEAQ   1253 TQGLPRVIELFEARRPKAKAVISEIDGVVRIEEGEDRLSVFVESEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQRTLKAIEEARKE 1501
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) RNA_pol_Rpb1_5-1ynnJ01 J:1253-1437                                                                                                                                                       ---------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) RNA_pol_Rpb1_5-1ynnJ02 J:1253-1437                                                                                                                                                       ---------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhh...............ee........eeeeee....eeeeee.........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhheeeee.........eee.....................eeee.....hhhhhh..hhhhhhhh.hhhhhhhhhhhh.......hhhhhhhh.....hhhhhhhhhh.eeehhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ynn J 1253 TQGLPRVIELFEARRPKAKAVISEIDGVVRIEEGEDRLSVFVESEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQRTLKAIEEARKE 1501
                                  1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412      1422      1432      1442      1452      1462      1472      1482      1492         


Chain K from PDB  Type:PROTEIN  Length:95
 aligned with RPOZ_THEAQ | Q9EVV4 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:95
                                    10        20        30        40        50        60        70        80        90     
          RPOZ_THEAQ      1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHRFKNTVLEPEERPKMRTLEGLYDDPNAVTWAMKELLTGRLFFGENLVPEDRLQKEMERLYPT   95
               SCOP domains d1ynnk1 K:1-95 RNA polymerase omega subunit                                                     SCOP domains
               CATH domains 1ynnK00 K:1-95  [code=3.90.940.10, no name defined]                                             CATH domains
               Pfam domains ------RNA_pol_Rpb6-1ynnK01 K:7-52                   ------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhh.............hhhhhhhhhhh....eee....hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                1ynn K    1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHRFKNTVLEPEERPKMRTLEGLYDDPNAVTWAMKELLTGRLFFGENLVPEDRLQKEMERLYPT   95
                                    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  (5, 7)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (9, 11)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (14, 18)

Asymmetric/Biological Unit
(-)
Clan: LEF-8-like (36)
(-)
Clan: RBP11-like (36)
(-)
Clan: no clan defined [family: RNA_pol_A_bac] (36)
(-)
Clan: no clan defined [family: RNA_pol_Rpb1_1] (37)
(-)
Clan: no clan defined [family: RNA_pol_Rpb1_2] (36)
(-)
Clan: no clan defined [family: RNA_pol_Rpb1_3] (36)
(-)
Clan: no clan defined [family: RNA_pol_Rpb1_4] (36)
(-)
Clan: no clan defined [family: RNA_pol_Rpb1_5] (36)
(-)
Clan: no clan defined [family: RNA_pol_Rpb2_1] (37)
(-)
Clan: no clan defined [family: RNA_pol_Rpb2_2] (36)
(-)
Clan: no clan defined [family: RNA_pol_Rpb2_3] (35)
(-)
Clan: no clan defined [family: RNA_pol_Rpb2_45] (8)
(-)
Clan: no clan defined [family: RNA_pol_Rpb2_7] (36)
(-)
Clan: no clan defined [family: RNA_pol_Rpb6] (37)

(-) Gene Ontology  (7, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RPOA_THEAQ | Q9KWU8)
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.

Chain C   (RPOB_THEAQ | Q9KWU7)
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 D,J   (RPOC_THEAQ | Q9KWU6)
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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain K   (RPOZ_THEAQ | Q9EVV4)
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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  1ynn
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  RPOC_THEAQ | Q9KWU6
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  RPOZ_THEAQ | Q9EVV4
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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
        RPOA_THEAQ | Q9KWU8: 1hqm 1i6v 1l9u 1l9z 1ynj 2gho 4xln 4xlp 4xlq 4xlr 4xls 5tjg
        RPOB_THEAQ | Q9KWU7: 1hqm 1i6v 1l9u 1l9z 1ynj 2gho 3mlq 4xax 4xln 4xlp 4xlq 4xlr 4xls 5tjg
        RPOC_THEAQ | Q9KWU6: 1hqm 1i6v 1l9u 1l9z 1ynj 2auj 2gho 4xln 4xlp 4xlq 4xlr 4xls 5tjg
        RPOZ_THEAQ | Q9EVV4: 1hqm 1i6v 1l9u 1l9z 1ynj 4xln 4xlp 4xlq 4xlr 4xls 5tjg

(-) Related Entries Specified in the PDB File

1ynj