| Structural highlights
6pmi is a 9 chain structure with sequence from Eco45, Eco57 and Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , |
| NonStd Res: | |
| Gene: | rpoA, Z4665, ECs4160 (ECO57), rpoB, ECS88_4448 (ECO45), rpoC, Z5561, ECs4911 (ECO57), rpoZ, ECS88_4064 (ECO45), fliA, flaD, rpoF, b1922, JW1907 (ECOLI) |
| Activity: | DNA-directed RNA polymerase, with EC number 2.7.7.6 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[RPOC_ECO57] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [RPOB_ECO45] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [RPOA_ECO57] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [RPOZ_ECO45] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. [FLIA_ECOLI] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor controls the expression of flagella-related genes.[HAMAP-Rule:MF_00962][1] [2] [3] [4]
Publication Abstract from PubMed
In bacteria, sigma(28) is the flagella-specific sigma factor that targets RNA polymerase (RNAP) to control the expression of flagella-related genes involving bacterial motility and chemotaxis. However, the structural mechanism of sigma(28) -dependent promoter recognition remains uncharacterized. Here, we report cryo-EM structures of E. coli sigma(28) -dependent transcribing complexes on a complete flagella-specific promoter. These structures reveal how sigma(28) -RNAP recognizes promoter DNA through strong interactions with the -10 element, but weak contacts with the -35 element, to initiate transcription. In addition, we observed a distinct architecture in which the beta' zinc-binding domain (ZBD) of RNAP stretches out from its canonical position to interact with the upstream non-template strand. Further in vitro and in vivo assays demonstrate that this interaction has the overall effect of facilitating closed-to-open isomerization of the RNAP-promoter complex by compensating for the weak interaction between sigma4 and -35 element. This suggests that ZBD relocation may be a general mechanism employed by sigma(70) family factors to enhance transcription from promoters with weak sigma4/-35 element interactions.
Structural basis of bacterial sigma(28) -mediated transcription reveals roles of the RNA polymerase zinc-binding domain.,Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B EMBO J. 2020 Jun 2:e104389. doi: 10.15252/embj.2020104389. PMID:32484956[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Arnosti DN, Chamberlin MJ. Secondary sigma factor controls transcription of flagellar and chemotaxis genes in Escherichia coli. Proc Natl Acad Sci U S A. 1989 Feb;86(3):830-4. doi: 10.1073/pnas.86.3.830. PMID:2644646 doi:http://dx.doi.org/10.1073/pnas.86.3.830
- ↑ Komeda Y. Transcriptional control of flagellar genes in Escherichia coli K-12. J Bacteriol. 1986 Dec;168(3):1315-8. doi: 10.1128/jb.168.3.1315-1318.1986. PMID:3536871 doi:http://dx.doi.org/10.1128/jb.168.3.1315-1318.1986
- ↑ Liu X, Matsumura P. An alternative sigma factor controls transcription of flagellar class-III operons in Escherichia coli: gene sequence, overproduction, purification and characterization. Gene. 1995 Oct 16;164(1):81-4. PMID:7590326
- ↑ Liu X, Matsumura P. Differential regulation of multiple overlapping promoters in flagellar class II operons in Escherichia coli. Mol Microbiol. 1996 Aug;21(3):613-20. doi: 10.1111/j.1365-2958.1996.tb02569.x. PMID:8866483 doi:http://dx.doi.org/10.1111/j.1365-2958.1996.tb02569.x
- ↑ Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B. Structural basis of bacterial sigma(28) -mediated transcription reveals roles of the RNA polymerase zinc-binding domain. EMBO J. 2020 Jun 2:e104389. doi: 10.15252/embj.2020104389. PMID:32484956 doi:http://dx.doi.org/10.15252/embj.2020104389
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