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(-) Description

Title :  STRUCTURE OF E. COLI RNA POLYMERASE BETA' G/G' INSERT
 
Authors :  M. Chlenov, S. Masuda, K. S. Murakami, V. Nikiforov, S. A. Darst, A. Mustaev
Date :  28 Aug 05  (Deposition) - 04 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  A (1x),B (1x),C (1x),D (1x),E (1x)
Biol. Unit 7:  A (1x),B (1x),C (1x),D (1x),E (1x)
Biol. Unit 8:  A,B,C,D,E  (1x)
Biol. Unit 9:  B (1x),C (1x),E (1x)
Biol. Unit 10:  A,D  (1x)
Biol. Unit 11:  A,B,C,D  (1x)
Keywords :  Sandwich-Barrel Hybrid Motif, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Chlenov, S. Masuda, K. S. Murakami, V. Nikiforov, S. A. Darst, A. Mustaev
Structure And Function Of Lineage-Specific Sequence Insertions In The Bacterial Rna Polymerase Beta' Subunit
J. Mol. Biol. V. 353 138 2005
PubMed-ID: 16154587  |  Reference-DOI: 10.1016/J.JMB.2005.07.073
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA-DIRECTED RNA POLYMERASE BETA' CHAIN
    Chains: A, B, C, D, E
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 5-190
    Gene: RPOC, TABB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RNAP BETA' SUBUNIT, TRANSCRIPTASE BETA' CHAIN, RNA POLYMERASE BETA' SUBUNIT

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E
Biological Unit 6 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)
Biological Unit 7 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)
Biological Unit 8 (1x): ABCDE
Biological Unit 9 (1x):  B (1x)C (1x) E (1x)
Biological Unit 10 (1x): A  D 
Biological Unit 11 (1x): ABCD 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2AUK)

(-) Sites  (0, 0)

(no "Site" information available for 2AUK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AUK)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AUK)

(-) Exons   (0, 0)

(no "Exon" information available for 2AUK)

(-) 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:189
 aligned with RPOC_ECOLI | P0A8T7 from UniProtKB/Swiss-Prot  Length:1407

    Alignment length:189
                                   949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119         
          RPOC_ECOLI    940 AASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQES 1128
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eee....eeeeee...eee.....eee.....eeeee.....eeeeee.....ee......ee....eeee....eeeee....eeeeee.......eeeee......eeeee...............eeeee................eee.....ee......ee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2auk A    1 GSHMAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQES  189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain B from PDB  Type:PROTEIN  Length:181
 aligned with RPOC_ECOLI | P0A8T7 from UniProtKB/Swiss-Prot  Length:1407

    Alignment length:181
                                   956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126 
          RPOC_ECOLI    947 ESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQE 1127
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eeeeee...eee.....eee....eeeeee.....eeeeeee....ee......ee....eeee.....eeee....eeeeee.......eeeee......eeeee.hhhhhhhhhhhh..eeeee................eee.....ee......ee....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2auk B    8 ESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQE  188
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 


Chain C from PDB  Type:PROTEIN  Length:183
 aligned with RPOC_ECOLI | P0A8T7 from UniProtKB/Swiss-Prot  Length:1407

    Alignment length:183
                                   955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125   
          RPOC_ECOLI    946 AESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQES 1128
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eeeeee...eee.....eee.....eeeee.....eeeeee.....ee......ee....eeee....eeeee....eeeeee.......eeeee......eeeee.hhhhhhhhhhh...eeeee.......ee....ee.eee.....ee......ee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2auk C    7 AESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQES  189
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186   


Chain D from PDB  Type:PROTEIN  Length:183
 aligned with RPOC_ECOLI | P0A8T7 from UniProtKB/Swiss-Prot  Length:1407

    Alignment length:183
                                   955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125   
          RPOC_ECOLI    946 AESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQES 1128
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eeeeee...eee.....eee.....eeeeee....eeeeee.....ee......ee....eeee....eeeee....eeeeee.......eeee........eeee...............eeeee................eee.....ee......ee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2auk D    7 AESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQES  189
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186   


Chain E from PDB  Type:PROTEIN  Length:188
 aligned with RPOC_ECOLI | P0A8T7 from UniProtKB/Swiss-Prot  Length:1407

    Alignment length:188
                                   950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120        
          RPOC_ECOLI    941 ASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQES 1128
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eee....eeeeee...eee.....eee....eeeeee.....eeeeeee....ee......ee....eeee.....eeee....eeeeee.......eeeee......eeeee.hhhhh.........eeeee................eee.....ee......ee....eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2auk E    2 SHMAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQES  189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   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 2AUK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (RPOC_ECOLI | P0A8T7)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000428    DNA-directed RNA polymerase complex    A protein complex that possesses DNA-directed RNA polymerase activity.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RPOC_ECOLI | P0A8T7: 2lmc 3iyd 3lu0 4iqz 4jk1 4jk2 4kmu 4kn4 4kn7 4mex 4mey 4xsx 4xsy 4xsz 4yg2 4yln 4ylo 4ylp 4zh2 4zh3 4zh4 5byh 5ezk 5ipl 5ipm 5ipn 5my1 5nsr 5nss 5uac 5uag 5uah 5uaj 5ual 5uaq 5up6 5upc 5vsw 5w1s 5w1t

(-) Related Entries Specified in the PDB File

2auj STRUCTURE OF THERMUS AQUATICUS RNA POLYMERASE BETA'-SUBUNIT INSERT