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(-) Description

Title :  STRUCTURE OF ESCHERICHIA COLI RNA POLYMERASE ALPHA SUBUNIT N-TERMINAL DOMAIN
 
Authors :  G. Zhang, S. A. Darst
Date :  08 May 98  (Deposition) - 11 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nucleotidyltransferase, Rnap, Alpha, Assemble (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Zhang, S. A. Darst
Structure Of The Escherichia Coli Rna Polymerase Alpha Subunit Amino-Terminal Domain.
Science V. 281 262 1998
PubMed-ID: 9657722  |  Reference-DOI: 10.1126/SCIENCE.281.5374.262
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA POLYMERASE ALPHA SUBUNIT
    Cell Line: BL-21
    Chains: A, B, C, D
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL-21
    Expression System Plasmid: PET15-B
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN RESIDUES 1-235
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1BDF)

(-) Sites  (0, 0)

(no "Site" information available for 1BDF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BDF)

(-) Exons   (0, 0)

(no "Exon" information available for 1BDF)

(-) 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:226
 aligned with RPOA_ECOLI | P0A7Z4 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 
           RPOA_ECOLI     2 QGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFV 232
               SCOP domains d1bdfa1 A:2-52,A:179-232 RNA polymerase alpha      d1bdfa2 A:53-178 RNA polymerase alpha subunit                                                                                 d1bdfa1 A:2-52,A:179-232 RNA polymerase alpha          SCOP domains
               CATH domains 1bdfA01 A:2-52,A:178-232                           1bdfA02 A:53-177 RNA Polymerase Alpha Subunit; Chain A, domain 2                                                             1bdfA01 A:2-52,A:178-232                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee....eeeeee......hhhhhhhhhhhhh......eeeeeeee................hhhhhhhhh..........eeeeeeeee..eeeehhh..............eeeee.....eeeeeeeeee......hhh..-----...............eeeeeee..............eeeeeee.....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bdf A   2 QGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRI-----ERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFV 232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       | -   |   171       181       191       201       211       221       231 
                                                                                                                                                                                       159   165                                                                   


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with RPOA_ECOLI | P0A7Z4 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
           RPOA_ECOLI     1 MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR 235
               SCOP domains d1bdfb1 B:1-52,B:179-235 RNA polymerase alpha       d1bdfb2 B:53-178 RNA polymerase alpha subunit                                                                                 d1bdfb1 B:1-52,B:179-235 RNA polymerase alpha             SCOP domains
               CATH domains -1bdfB01 B:2-52,B:178-231                           1bdfB02 B:53-177 RNA Polymerase Alpha Subunit; Chain A, domain 2                                                             1bdfB01 B:2-52,B:178-231                              ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee....eeeeee......hhhhhhhhhhhhh......eeeeeeee................hhhhhhhhh...eee....eeeeeeeeee.eeeehhh......eee.....eeeee....eeeeeeeeeee.......hhh..---................eeeeeee..............eeeeeee.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bdf B   1 MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH---DERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   |   170       180       190       200       210       220       230     
                                                                                                                                                                                         160 164                                                                       


Chain C from PDB  Type:PROTEIN  Length:228
 aligned with RPOA_ECOLI | P0A7Z4 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
           RPOA_ECOLI     1 MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR 235
               SCOP domains d1bdfc1 C:1-52,C:179-235 RNA polymerase alpha       d1bdfc2 C:53-178 RNA polymerase alpha subunit                                                                                 d1bdfc1 C:1-52,C:179-235 RNA polymerase alpha             SCOP domains
               CATH domains -1bdfC01 C:2-52,C:178-231                           1bdfC02 C:53-177 RNA Polymerase Alpha Subunit; Chain A, domain 2                                                             1bdfC01 C:2-52,C:178-231                              ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee....eeeeee......hhhhhhhhhhhhh......eeeeeeee................hhhhhhhhh...eee....eeeeeeeee..eeeehhh......eee.....eeeee.....eeeeeeeeee............-------............eeeeeee..............eeeeeee.....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bdf C   1 MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH-------IGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
                                                                                                                                                                                         160     168                                                                   


Chain D from PDB  Type:PROTEIN  Length:231
 aligned with RPOA_ECOLI | P0A7Z4 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
           RPOA_ECOLI     1 MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR 235
               SCOP domains d1bdfd1 D:1-52,D:179-235 RNA polymerase alpha       d1bdfd2 D:53-178 RNA polymerase alpha subunit                                                                                 d1bdfd1 D:1-52,D:179-235 RNA polymerase alpha             SCOP domains
               CATH domains 1bdfD01 D:1-52,D:178-231                            1bdfD02 D:53-177 RNA Polymerase Alpha Subunit; Chain A, domain 2                                                             1bdfD01 D:1-52,D:178-231                              ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee....eeeeee......hhhhhhhhhhhhh......eeeeeeee................hhhhhhhhh...eee....eeeeeeeee..eeeehhh......eee.....eeeee.....eeeeeeeeee............----...............eeeeeee..............eeeeeee.....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bdf D   1 MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIH----ERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    |  170       180       190       200       210       220       230     
                                                                                                                                                                                         160  165
   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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BDF)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RPOA_ECOLI | P0A7Z4)
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: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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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
        RPOA_ECOLI | P0A7Z4: 1coo 1lb2 1xs9 2jzb 3iyd 3k4g 3lu0 3n4m 3n97 4jk1 4jk2 4kmu 4kn4 4kn7 4mex 4mey 4s20 4xsx 4xsy 4xsz 4yg2 4yln 4ylo 4ylp 4zh2 4zh3 4zh4 5byh 5ciz 5ezk 5ipl 5ipm 5ipn 5ms0 5my1 5nsr 5nss 5uac 5uag 5uah 5uaj 5ual 5uaq 5up6 5upc 5vsw 5w1s 5w1t

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