Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family

Thaw, Paul; Sedelnikova, Svetlana E.; Muranova, T. A.; Wiese, Sebastian; Ayora, Silvia; Alonso, Juan C.; Brinkman, Arie B.; Akerboom, Jasper; Oost, John van der; Rafferty, John B.

doi:10.1093/nar/gkl009

Cited by 108 publications

(121 citation statements)

References 52 publications

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“…DM1 (Leonard et al, 2001;Koike et al, 2003;Thaw et al, 2006) revealed that the four dimers are arranged as a disc. In the structure of the Pyrococcus sp.…”

Section: Crystallization Data Processing and Structurementioning

confidence: 99%

“…FL11, E. coli AsnC and Bacillus subtilis LrpC, have been determined (Leonard et al, 2001;Koike et al, 2004: Thaw et al, 2006. The proteins consist of an N-terminal helix-turn-helix DNA-binding domain connected by a hinge to the C-terminal RAM (regulation of amino-acid metabolism) domain, with a fold.…”

Section: Introductionmentioning

confidence: 99%

“…The Lrp/AsnCfamily proteins form symmetric dimers, mainly through interactions between the antiparallel -sheets of the C-terminal RAM domain. The LrpA, AsnC and LrpC structures revealed four dimers are arranged as a disc, with their RAM domains contacting in the centre and their N-terminal domains facing outward (Leonard et al, 2001;Thaw et al, 2006). In the case of the FL11 protein, the dimers form a sixfold helix, also with the RAM domains facing toward the centre and the N-terminal domains facing outward (Koike et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

“…The RAM domain of the Lrp/AsnC-family proteins may be involved in their effector-dependent allosteric regulation (Brinkman et al, 2003). In fact, bound asparagine molecules were found in the RAM domain of E. coli AsnC (Thaw et al, 2006). Archaea and bacteria also have proteins bearing the RAM domain, but lacking the DNA-binding domain.…”

Section: Introductionmentioning

confidence: 99%

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Structure of the stand-alone RAM-domain protein fromThermus thermophilusHB8

et al. 2006

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PDB Reference: TTHA0845, 2djw, r2djwsf.The stand-alone RAM (regulation of amino-acid metabolism) domain protein SraA from Thermus thermophilus HB8 (TTHA0845) was crystallized in the presence of zinc ions. The X-ray crystal structure was determined using a multiple-wavelength anomalous dispersion technique and was refined at 2.4 Å resolution to a final R factor of 25.0%. The monomeric structure is a fold and it dimerizes mainly through interactions between the antiparallelsheets. Furthermore, five SraA dimers form a ring with external and internal diameters of 70 and 20 Å , respectively. This decameric structure is unique compared with the octameric and dodecameric structures found for other standalone RAM-domain proteins and the C-terminal RAM domains of Lrp/AsnCfamily proteins.

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“…DM1 (Leonard et al, 2001;Koike et al, 2003;Thaw et al, 2006) revealed that the four dimers are arranged as a disc. In the structure of the Pyrococcus sp.…”

Section: Crystallization Data Processing and Structurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Structure of the stand-alone RAM-domain protein fromThermus thermophilusHB8

et al. 2006

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“…Crystal structures have been reported for FFRPs from Pyrococcus sp. OT3, Bacillus subtilis, Escherichia coli, Neisseria meningitides, M. tuberculosis and Sulfolobus tokodaii (Leonard et al, 2001;Koike et al, 2004;Thaw et al, 2006;Ren et al, 2007;Shrivastava & Ramachandran, 2007;Shrivastava et al, 2009;Nakano et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Cloning, overexpression, purification and preliminary X-ray analysis of a feast/famine regulatory protein (Rv2779c) fromMycobacterium tuberculosisH37Rv

Dey

Ramachandran

2013

Acta Cryst Sect F

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Rv2779c from Mycobacterium tuberculosis is a feast/famine regulatory protein. This class of proteins are also known as the leucine-responsive regulatory protein/asparagine synthase C family (Lrp/AsnC) of transcriptional regulators and are known to be involved in various metabolic processes in bacteria and fungi. They contain a RAM (regulator of amino-acid metabolism) domain that is rarely found in humans and acts as the oligomerization domain. Since the oligomeric status is often linked to the particular functional role in these proteins, binding of ligands to the domain can elicit specific functional responses. Full-length Rv2779c corresponding to a molecular mass of 19.8 kDa and 179 residues was cloned and purified to homogeneity following transformation into Escherichia coli C41 (DE3) cells. Crystals were grown by vapour diffusion using the hanging-drop method. Diffraction data extending to 2.8 Å resolution were collected from a single crystal that belonged to space group P2 1 2 1 2, with unitcell parameters a = 99.6, b = 146.0, c = 49.9 Å . Matthews coefficient (V M ) calculations suggest that four molecules are present in the asymmetric unit, corresponding to a solvent content of $46%. Molecular-replacement calculations using the crystal structure of a homologue, Rv3291c, as the search model gave an unambiguous solution corresponding to four subunits in the asymmetric unit.

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Siroheme Decarboxylase in Complex with Iron‐Uroporphyrin III

Layer

2016

Encyclopedia of Inorganic and Bioinorganic Chemistry

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Siroheme decarboxylase catalyzes the conversion of siroheme to 12,18‐didecarboxysiroheme during heme d 1 biosynthesis in denitrifying bacteria and during the alternative heme biosynthesis in archaea and sulfate‐reducing bacteria. The crystal structure of siroheme decarboxylase from Hydrogenobacter thermophilus in complex with the substrate analog iron‐uroporphyrin III is available as well as the structure of siroheme decarboxylase from Desulfovibrio desulfuricans in complex with the reaction product didecarboxysiroheme. The two structures reveal two possible binding modes for the iron‐containing tetrapyrroles. In both cases, the central iron ion is coordinated by a histidine residue as the axial ligand, however, these histidines are located at different positions of the enzyme. Moreover, although identical amino acid residues coordinate the substrate analog and reaction product, the respective equivalent residues interact with different parts of the respective tetrapyrrole macrocycle. The two observed tetrapyrrole binding modes might hint toward two different binding sites for the initial substrate, siroheme, and the reaction intermediate monodecarboxysiroheme.

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Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family

Cited by 108 publications

References 52 publications

Structure of the stand-alone RAM-domain protein fromThermus thermophilusHB8

Structure of the stand-alone RAM-domain protein fromThermus thermophilusHB8

Cloning, overexpression, purification and preliminary X-ray analysis of a feast/famine regulatory protein (Rv2779c) fromMycobacterium tuberculosisH37Rv

Siroheme Decarboxylase in Complex with Iron‐Uroporphyrin III

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