4jkr | pdb_00004jkr

Crystal Structure of E. coli RNA Polymerase in complex with ppGpp

spinqualitylabelsall models 4jkr, resolution 4.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4jkr is a 12 chain structure with sequence from Escherichia coli bw2952, Escherichia coli dh1, Escherichia coli k-12 and Escherichia coli o104:h4 str. 2009el-2071. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: G4P, SR, ZN Gene: ECDH10B_3470, O3O_23125, rpoA (Escherichia coli O104:H4 str. 2009EL-2071), ECDH1ME8569_3846, EcDH1_4008, O3K_23925, rpoB (Escherichia coli DH1), BWG_3647, O3O_01425, rpoC (Escherichia coli BW2952), ECDH1ME8569_3534, EcDH1_0056, O3O_25075, rpoZ (Escherichia coli DH1), alt, b3067, JW3039, rpoD (Escherichia coli K-12) Activity: DNA-directed RNA polymerase, with EC number 2.7.7.6 Resources: FirstGlance, OCA, RCSB, PDBsum Function [C9QUL2_ECOD1] 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:SAAS012293_004_017283] [K0BPQ3_ECO1E] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_00059] [C5A0S8_ECOBW] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[SAAS:SAAS012754_004_011999] [C9QV90_ECOD1] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_01321][RuleBase:RU000432] [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 Guanosine tetraphosphate (ppGpp) is an alarmone that enables bacteria to adapt to their environment. It has been known for years that ppGpp acts directly on RNA polymerase (RNAP) to alter the rate of transcription, but its exact target site is still under debate. Here we report a crystal structure of Escherichia coli RNAP holoenzyme in complex with ppGpp at 4.5 A resolution. The structure reveals that ppGpp binds at an interface between the shelf and core modules on the outer surface of RNAP, away from the catalytic center and the nucleic acid binding path. Bound ppGpp connects these two pivotal modules that may restrain the opening of the RNAP cleft. A detailed mechanism of action of ppGpp is proposed in which ppGpp prevents the closure of the active center that is induced by the binding of NTP, which could slow down nucleotide addition cycles and destabilize the initial transcription complexes. The Mechanism of E. coli RNA Polymerase Regulation by ppGpp Is Suggested by the Structure of their Complex.,Zuo Y, Wang Y, Steitz TA Mol Cell. 2013 May 9;50(3):430-6. doi: 10.1016/j.molcel.2013.03.020. Epub 2013, Apr 25. PMID:23623685 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also RNA polymerase

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