4jk1 | pdb_00004jk1

X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with Guanosine tetraphosphate (ppGpp)

spinqualitylabelsall models 4jk1, resolution 3.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4jk1 is a 12 chain structure with sequence from Escherichia coli k-12 and Escherichia coli str. k-12 substr. mds42. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: G4P, ZN Related: 4igc, 4jk2 Gene: rpoA, pez, phs, sez, b3295, JW3257 (Escherichia coli K-12), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 (Escherichia coli K-12), rpoC, tabB, b3988, JW3951 (Escherichia coli K-12), rpoZ, ECMDS42_3083 (Escherichia coli str. K-12 substr. MDS42), rpoD, alt, b3067, JW3039 (Escherichia coli K-12) Activity: DNA-directed RNA polymerase, with EC number 2.7.7.6 Resources: FirstGlance, OCA, RCSB, PDBsum Function [H0QDQ9_ECOLI] 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 (By similarity).[HAMAP-Rule:MF_00366][SAAS:SAAS003716_004_017283] [RPOA_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] [RPOC_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [RPOB_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [RPOD_ECOLI] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium. Publication Abstract from PubMed Both ppGpp and pppGpp are thought to function collectively as second messengers for many complex cellular responses to nutritional stress throughout biology. There are few indications that their regulatory effects might be different; however, this question has been largely unexplored for lack of an ability to experimentally manipulate the relative abundance of ppGpp and pppGpp. Here, we achieve preferential accumulation of either ppGpp or pppGpp with Escherichia coli strains through induction of different Streptococcal (p)ppGpp synthetase fragments. In addition, expression of E. coli GppA, a pppGpp 5'-gamma phosphate hydrolase that converts pppGpp to ppGpp, is manipulated to fine tune differential accumulation of ppGpp and pppGpp. In vivo and in vitro experiments show that pppGpp is less potent than ppGpp with respect to regulation of growth rate, RNA/DNA ratios, ribosomal RNA P1 promoter transcription inhibition, threonine operon promoter activation and RpoS induction. To provide further insights into regulation by (p)ppGpp, we have also determined crystal structures of E. coli RNA polymerase-sigma70 holoenzyme with ppGpp and pppGpp. We find that both nucleotides bind to a site at the interface between beta' and omega subunits. Differential regulation by ppGpp versus pppGpp in Escherichia coli.,Mechold U, Potrykus K, Murphy H, Murakami KS, Cashel M Nucleic Acids Res. 2013 Apr 25. PMID:23620295 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also RNA polymerase

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