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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI RNA POLYMERASE BETA SUBUNIT BETA2-BETAI4 DOMAINS
 
Authors :  S. A. Darst, N. Opalka
Date :  16 Feb 10  (Deposition) - 20 Oct 10  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Bbm2, Dna-Directed Rna Polymerase, Nucleotidyltransferase, Transcription, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Opalka, J. Brown, W. J. Lane, K. A. Twist, R. Landick, F. J. Asturias, S. A. Darst
Complete Structural Model Of Escherichia Coli Rna Polymeras From A Hybrid Approach.
Plos Biol. V. 8 00483 2010
PubMed-ID: 20856905  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1000483

(-) Compounds

Molecule 1 - DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA
    Chains: A
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BETA2-BETA-I-4 DOMAINS
    Gene: B3987, GRON, JW3950, NITB, RIF, RON, RPOB, STL, STV, TABD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: RNAP SUBUNIT BETA, TRANSCRIPTASE SUBUNIT BETA, RNA POLYMERASE SUBUNIT BETA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric/Biological Unit (2, 17)
No.NameCountTypeFull Name
1MLY10Mod. Amino AcidN-DIMETHYL-LYSINE
2MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3LTI)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LTI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LTI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LTI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LTI)

(-) Exons   (0, 0)

(no "Exon" information available for 3LTI)

(-) 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:284
 aligned with RPOB_ECOLI | P0A8V2 from UniProtKB/Swiss-Prot  Length:1342

    Alignment length:293
                                   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   
           RPOB_ECOLI   151 RSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVD 443
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -RNA_pol_R         pb2_1-3ltiA01 A:152-443                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_pol_Rpb2_2-3ltiA02 A:329-443                                                                                    Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_pol_Rpb2_2-3ltiA03 A:329-443                                                                                    Pfam domains (3)
         Sec.struct. author ...eeeeee.---------..eeeeee......eeeee.....eeeee.....eehhhhhhhh..hhhhhhhhhh.eeeeeee..eeeee.hhhhhh.......eee..eeee......hhhhhhhhhhh...eee.hhhhhhh......ee......eee......hhhhhhhhhhh...eeeee........hhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lti A 151 mSPGVFFDSD---------VLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQmELVPERLRGETASFDIEANGkVYVEkGRRITARHIRQLEKDDVKLIEVPVEYIAGkVVAkDYIDESTGELICAANmELSLDLLAkLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRmmRPGEPPTREAAESLFENLFFSEDRYDLSAVGRmkFNRSLLREEIEGSGILSkDDIIDVmkkLIDIRNGkGEVD 443
                            |      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   
                            |      160       170                                                                  239-MSE              260-MLY|                           295-MLY             315-MSE  324-MLY                                      369-MSE                           403-MSE            422-MLY  |||     439-MLY
                          151-MSE                                                                                                           265-MLY                           299-MLY                                                                370-MSE                           404-MLY                  429-MSE          
                                                                                                                                                                                                                                                                                                                 430-MLY         
                                                                                                                                                                                                                                                                                                                  431-MLY
   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 3LTI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LTI)

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RNA_pol_Rpb2_1] (37)
(-)
Clan: no clan defined [family: RNA_pol_Rpb2_2] (36)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RPOB_ECOLI | P0A8V2)
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: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.
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
        RPOB_ECOLI | P0A8V2: 3iyd 3lu0 3t72 3tbi 4jk1 4jk2 4kmu 4kn4 4kn7 4mex 4mey 4s20 4xsx 4xsy 4xsz 4yg2 4yln 4ylo 4ylp 4zh2 4zh3 4zh4 5byh 5ezk 5ipl 5ipm 5ipn 5ms0 5nsr 5nss 5uac 5uag 5uah 5uaj 5ual 5uaq 5up6 5upc 5vsw 5w1s 5w1t

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