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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THERMUS THERMOPHILUS TRANSCRIPTION-REPAIR COUPLING FACTOR RNA POLYMERASE INTERACTING DOMAIN WITH THE THERMUS AQUATICUS RNA POLYMERASE BETA1 DOMAIN
 
Authors :  S. A. Darst, L. F. Westblade, E. A. Campbell
Date :  18 Apr 10  (Deposition) - 13 Oct 10  (Release) - 19 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.91
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Tudor, Transferase-Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. F. Westblade, E. A. Campbell, C. Pukhrambam, J. C. Padovan, B. E. Nickels, V. Lamour, S. A. Darst
Structural Basis For The Bacterial Transcription-Repair Coupling Factor/Rna Polymerase Interaction.
Nucleic Acids Res. V. 38 8357 2010
PubMed-ID: 20702425  |  Reference-DOI: 10.1093/NAR/GKQ692

(-) Compounds

Molecule 1 - DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA
    Chains: A, B, C, D
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A-BASED
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BETA1 DOMAIN (UNP RESIDUES 17-139 AND 334-395)
    Gene: RPOB
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: RNAP SUBUNIT BETA, TRANSCRIPTASE SUBUNIT BETA, RNA POLYMERASE SUBUNIT BETA
 
Molecule 2 - TRANSCRIPTION-REPAIR COUPLING FACTOR
    Chains: E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A-BASED
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RNA POLYMERASE INTERACTING DOMAIN (UNP RESIDUES 321-387)
    Gene: MFD, TT_C0533
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A   E   
Biological Unit 2 (1x):  B   F  
Biological Unit 3 (1x):   C   G 
Biological Unit 4 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:343 , ARG A:350 , GLU A:384 , LEU B:18 , THR B:19BINDING SITE FOR RESIDUE PO4 A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln C:139 -Gly C:332
2Phe D:52 -Pro D:53
3Gln D:139 -Gly D:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MLQ)

(-) 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:186
 aligned with RPOB_THEAQ | Q9KWU7 from UniProtKB/Swiss-Prot  Length:1119

    Alignment length:378
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386        
           RPOB_THEAQ    17 PLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQF 394
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhh.eee.......eeeeeeeeee.....hhhhhhhh....eeeeeeeeeeee.....eeeeeeeeeeee.......eee..eeee....---------------------------------------------------------------------------------------------------------..---------------------------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mlq A  17 PLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQ---------------------------------------------------------------------------------------------------------GG---------------------------------------------------------------------------------------RTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQF 394
                                    26        36        46        56        66        76        86        96       106       116       126       136  |      -         -         -         -         -         -         -         -         -         -       333         -         -         -         -         -         -         -         -       336       346       356       366       376       386        
                                                                                                                                                    139                                                                                                       332|                                                                                     334                                                            
                                                                                                                                                                                                                                                               333                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with RPOB_THEAQ | Q9KWU7 from UniProtKB/Swiss-Prot  Length:1119

    Alignment length:376
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386      
           RPOB_THEAQ    17 PLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLS 392
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhheeee.----..eeeeeeeeee.....hhhhhhhhh...eeeeeeeeeeee.....eeeeeeeeeeee.......eee..eeee....---------------------------------------------------------------------------------------------------------..---------------------------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mlq B  17 PLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEG----GGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQ---------------------------------------------------------------------------------------------------------GG---------------------------------------------------------------------------------------RTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLS 392
                                    26        36        46        56|    |  66        76        86        96       106       116       126       136  |      -         -         -         -         -         -         -         -         -         -       333         -         -         -         -         -         -         -         -       336       346       356       366       376       386      
                                                                   57   62                                                                          139                                                                                                       332|                                                                                     334                                                          
                                                                                                                                                                                                                                                               333                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:182
 aligned with RPOB_THEAQ | Q9KWU7 from UniProtKB/Swiss-Prot  Length:1119

    Alignment length:378
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386        
           RPOB_THEAQ    17 PLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQF 394
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...hhhhh..hhhhhhhhh...eee.----..eeeeeeeeee.....hhhhhhhhh...eeeeeeeeeeee.....eeeeeeeeeeee.......eee..eeee....---------------------------------------------------------------------------------------------------------..---------------------------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mlq C  17 PLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEG----GGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQ---------------------------------------------------------------------------------------------------------GG---------------------------------------------------------------------------------------RTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQF 394
                                    26        36        46        56|    |  66        76        86        96       106       116       126       136  |      -         -         -         -         -         -         -         -         -         -       333         -         -         -         -         -         -         -         -       336       346       356       366       376       386        
                                                                   57   62                                                                          139                                                                                                       332|                                                                                     334                                                            
                                                                                                                                                                                                                                                               333                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:185
 aligned with RPOB_THEAQ | Q9KWU7 from UniProtKB/Swiss-Prot  Length:1119

    Alignment length:378
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385        
           RPOB_THEAQ    16 PPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQ 393
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -RNA_pol_Rpb2_1-3mlqD01 D:17-389                                                                                                                                                                                                                                                                                                                                                      ---- Pfam domains (1)
           Pfam domains (2) -RNA_pol_Rpb2_1-3mlqD02 D:17-389                                                                                                                                                                                                                                                                                                                                                      ---- Pfam domains (2)
           Pfam domains (3) -RNA_pol_Rpb2_1-3mlqD03 D:17-389                                                                                                                                                                                                                                                                                                                                                      ---- Pfam domains (3)
           Pfam domains (4) -RNA_pol_Rpb2_1-3mlqD04 D:17-389                                                                                                                                                                                                                                                                                                                                                      ---- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhh.ee...-....eeeeeeeeee.....hhhhhhhh....eeeeeeeeeeee.....eeeeeeeeeeee.......eee..eeee....---------------------------------------------------------------------------------------------------------..---------------------------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mlq D  16 MPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGD-GKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQ---------------------------------------------------------------------------------------------------------GG---------------------------------------------------------------------------------------RTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQ 393
                                    25        35        45        55  | |   65        75        85        95       105       115       125       135   |     -         -         -         -         -         -         -         -         -         -       332|        -         -         -         -         -         -         -         -       335       345       355       365       375       385        
                                                                     58 |                                                                            139                                                                                                       332|                                                                                     334                                                           
                                                                       60                                                                                                                                                                                       333                                                                                                                                                   


Chain E from PDB  Type:PROTEIN  Length:38
 aligned with Q72KB4_THET2 | Q72KB4 from UniProtKB/TrEMBL  Length:978

    Alignment length:38
                                   341       351       361        
         Q72KB4_THET2   332 VGQYLGLETREVLGVKRDYLVLRYKGEGKLYLPVEQLP 369
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..eeeeeeeeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 3mlq E 332 VGQYLGLETREVLGVKRDYLVLRYKGEGKLYLPVEQLP 369
                                   341       351       361        


Chain F from PDB  Type:PROTEIN  Length:30
 aligned with Q72KB4_THET2 | Q72KB4 from UniProtKB/TrEMBL  Length:978

    Alignment length:37
                                   342       352       362       
         Q72KB4_THET2   333 GQYLGLETREVLGVKRDYLVLRYKGEGKLYLPVEQLP 369
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.-------..eeeeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 3mlq F 333 GQYLGLET-------RDYLVLRYKGEGKLYLPVEQLP 369
                                   | -     | 352       362       
                                 340     348                     


Chain G from PDB  Type:PROTEIN  Length:40
 aligned with Q72KB4_THET2 | Q72KB4 from UniProtKB/TrEMBL  Length:978

    Alignment length:40
                                   338       348       358       368
         Q72KB4_THET2   329 EHGVGQYLGLETREVLGVKRDYLVLRYKGEGKLYLPVEQL 368
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..........eeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 3mlq G 329 EHGVGQYLGLETREVLGVKRDYLVLRYKGEGKLYLPVEQL 368
                                   338       348       358       368


Chain H from PDB  Type:PROTEIN  Length:42
 aligned with Q72KB4_THET2 | Q72KB4 from UniProtKB/TrEMBL  Length:978

    Alignment length:42
                                   343       353       363       373  
         Q72KB4_THET2   334 QYLGLETREVLGVKRDYLVLRYKGEGKLYLPVEQLPLLKRHP 375
               SCOP domains ------------------------------------------ SCOP domains
               CATH domains ------------------------------------------ CATH domains
           Pfam domains (1) CarD_CdnL_TRCF-3mlqH01 H:334-375           Pfam domains (1)
           Pfam domains (2) CarD_CdnL_TRCF-3mlqH02 H:334-375           Pfam domains (2)
           Pfam domains (3) CarD_CdnL_TRCF-3mlqH03 H:334-375           Pfam domains (3)
           Pfam domains (4) CarD_CdnL_TRCF-3mlqH04 H:334-375           Pfam domains (4)
         Sec.struct. author .eeeeeeee....eeeeeeee.....eeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------ PROSITE
                 Transcript ------------------------------------------ Transcript
                 3mlq H 334 QYLGLETREVLGVKRDYLVLRYKGEGKLYLPVEQLPLLKRHP 375
                                   343       353       363       373
   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 3MLQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: no clan defined [family: CarD_CdnL_TRCF] (1)
(-)
Clan: no clan defined [family: RNA_pol_Rpb2_1] (37)

(-) Gene Ontology  (17, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 E,F,G,H   (Q72KB4_THET2 | Q72KB4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0000716    transcription-coupled nucleotide-excision repair, DNA damage recognition    The identification of lesions on the actively transcribed strand of the DNA duplex as well as a small subset of lesions not recognized by the general nucleotide-excision repair pathway.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  Cis Peptide Bonds
    Gln C:139 - Gly C:332   [ RasMol ]  
    Gln D:139 - Gly D:332   [ RasMol ]  
    Phe D:52 - Pro D:53   [ RasMol ]  
 
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  3mlq
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  Q72KB4_THET2 | Q72KB4
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  RPOB_THEAQ | Q9KWU7
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  2.7.7.6
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  Q72KB4_THET2 | Q72KB4
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  RPOB_THEAQ | Q9KWU7
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPOB_THEAQ | Q9KWU7: 1hqm 1i6v 1l9u 1l9z 1ynj 1ynn 2gho 4xax 4xln 4xlp 4xlq 4xlr 4xls 5tjg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3MLQ)