Brand  (β version)

PDB ID: 5D4D

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Ligands
Code Name Style Show Link
MG Magnesium ion PoSSuM
ZN Zinc ion PoSSuM
C Cytidine-5'-monophosphate PoSSuM
CTP Cytidine-5'-triphosphate PoSSuM
NAD Nicotinamide-adenine-dinucleotide PoSSuM
Non-standard Residues
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Glycosylation
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Structure summary

Code : 5D4D   PDBj   RCSB PDB   PDBe
Header : transcription/dna
Title : Crystal structure of Thermus thermophilus product complex for transcription initiation with NAD and CTP
Release Data : 2016-07-06
Compound :
mol_id molecule chains synonym
1 DNA-directed RNA polymerase subunit alpha A,B,K,L RNAP subunit alpha,RNA polymerase subunit alpha,Transcriptase subunit alpha
ec: 2.7.7.6
mol_id molecule chains synonym
2 DNA-directed RNA polymerase subunit beta C,M RNAP subunit beta,RNA polymerase subunit beta,Transcriptase subunit beta
ec: 2.7.7.6
mol_id molecule chains synonym
3 DNA-directed RNA polymerase subunit beta' D,N RNAP subunit beta',RNA polymerase subunit beta',Transcriptase subunit beta'
ec: 2.7.7.6
mol_id molecule chains synonym
4 DNA-directed RNA polymerase subunit omega E,O RNAP omega subunit,RNA polymerase omega subunit,Transcriptase subunit omega
ec: 2.7.7.6
mol_id molecule chains
5 RNA polymerase sigma factor SigA F,P
mol_id molecule chains
6 DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') G,R
mol_id molecule chains
7 DNA (27-MER) H,S
Source :
mol_id organism_scientific
1 Thermus thermophilus  (taxid:274)
mol_id organism_scientific
2 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)  (taxid:300852)
strain: HB8 / ATCC 27634 / DSM 579
mol_id organism_scientific
3 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)  (taxid:300852)
strain: HB8 / ATCC 27634 / DSM 579
mol_id organism_scientific
4 Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)  (taxid:300852)
strain: HB8 / ATCC 27634 / DSM 579
mol_id organism_scientific expression_system
5 Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)  (taxid:262724) Escherichia coli  (taxid:562)
strain: HB27 / ATCC BAA-163 / DSM 7039
gene: sigA, rpoD, TT_C0164
expression_system_strain: BL21(DE3)
expression_system_vector_type: plsamid
expression_system_plasmid: pET28a
mol_id organism_scientific
6 Thermus thermophilus  (taxid:274)
synthetic: yes
mol_id organism_scientific
7 Thermus thermophilus  (taxid:274)
synthetic: yes
Authors : Zhang, Y., Ebright, R.H.
Keywords : RNA polymerase, transcription initiation, bacterial, NCIN, non-canonical initiating nucleotide, primer-dependent initiation, DNA, Single-Stranded, DNA-Directed RNA Polymerases, Gene Expression Regulation, Promoter Regions, Genetic, Protein Conformation, Sigma Factor, transcription-dna complex
Exp. method : X-RAY DIFFRACTION ( 3.0 Å )
Citation :

The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.

Bird, J.G.,Zhang, Y.,Tian, Y.  et al.
(2016)  Nature  535 : 444 - 447

PubMed: 27383794
DOI: 10.1038/nature18622

Reaction

Chain : A, B, K, L
UniProt : Q9Z9H6 (RPOA_THETH)
Reaction: EC: Evidence:
Physiological Direction:
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate 2.7.7.6 -
-
Chain : C, M
UniProt : Q8RQE9 (RPOB_THET8)
Reaction: EC: Evidence:
Physiological Direction:
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate 2.7.7.6 HAMAP-Rule:MF_01321
-
Chain : D, N
UniProt : Q8RQE8 (RPOC_THET8)
Reaction: EC: Evidence:
Physiological Direction:
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate 2.7.7.6 HAMAP-Rule:MF_01322
-
Cofactor: Evidence: Note:
Mg(2+) ECO:0000255 | HAMAP-Rule:MF_01322
Binds 1 Mg(2+) ion per subunit.
Zn(2+) ECO:0000255 | HAMAP-Rule:MF_01322
Binds 2 Zn(2+) ions per subunit.
Chain : E, O
UniProt : Q8RQE7 (RPOZ_THET8)
Reaction: EC: Evidence:
Physiological Direction:
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate 2.7.7.6 HAMAP-Rule:MF_00366
-
Chain : F, P
UniProt : Q72L95 (SIGA_THET2)
Reaction : -