MINT MINT, Dpt of Biology, University of Rome Tor Vergata MINT http://mint.bio.uniroma2.it/mint url>http://mint.bio.uniroma2.it/mint/ https://mint.bio.uniroma2.it MINT-[0-9]+ https://mint.bio.uniroma2.it/index.php/results-interactions/?id=${ac} The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO J. (0261-4189) 2011 imex curation Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M., Thibault G., Liu K., Ramachandran S., Snider J., Pai EF., Houry WA. Only protein-protein interactions in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M., Thibault G., Liu K., Ramachandran S., Snider J., Pai EF., Houry WA. EMBO J. (0261-4189) 2011 Only protein-protein interactions imex curation Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO J. (0261-4189) 2011 imex curation Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M., Thibault G., Liu K., Ramachandran S., Snider J., Pai EF., Houry WA. Only protein-protein interactions in vitro In vitro electron microscopy electron microscopy Electron crystallography Electron cryomicroscopy Electron crystallography Electron cryomicroscopy predetermined predetermined participant predetermined Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M., Thibault G., Liu K., Ramachandran S., Snider J., Pai EF., Houry WA. EMBO J. (0261-4189) 2011 Only protein-protein interactions imex curation Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO J. (0261-4189) 2011 imex curation Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M., Thibault G., Liu K., Ramachandran S., Snider J., Pai EF., Houry WA. Only protein-protein interactions in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M., Thibault G., Liu K., Ramachandran S., Snider J., Pai EF., Houry WA. EMBO J. (0261-4189) 2011 Only protein-protein interactions imex curation Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO J. (0261-4189) 2011 imex curation Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M., Thibault G., Liu K., Ramachandran S., Snider J., Pai EF., Houry WA. Only protein-protein interactions in vitro In vitro solution sedimentati cosedimentation in solution solution sedimentati predetermined predetermined participant predetermined Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M., Thibault G., Liu K., Ramachandran S., Snider J., Pai EF., Houry WA. EMBO J. (0261-4189) 2011 Only protein-protein interactions imex curation Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO J. (0261-4189) 2011 imex curation Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M., Thibault G., Liu K., Ramachandran S., Snider J., Pai EF., Houry WA. Only protein-protein interactions in vitro In vitro crosslink cross-linking study crosslink predetermined predetermined participant predetermined Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M., Thibault G., Liu K., Ramachandran S., Snider J., Pai EF., Houry WA. EMBO J. (0261-4189) 2011 Only protein-protein interactions imex curation ldci_ecoli Inducible lysine decarboxylase cadA b4131 ldcI JW4092 protein protein ecoli Escherichia coli (strain K12) MNVIAILNHMGVYFKEEPIRELHRALERLNFQIVYPNDRDDLLKLIENNARLCGVIFDWDKYNLELCEEISKMNENLPLYAFANTYSTLDVSLNDLRLQISFFEYALGAAEDIANKIKQTTDEYINTILPPLTKALFKYVREGKYTFCTPGHMGGTAFQKSPVGSLFYDFFGPNTMKSDISISVSELGSLLDHSGPHKEAEQYIARVFNADRSYMVTNGTSTANKIVGMYSAPAGSTILIDRNCHKSLTHLMMMSDVTPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETPNATWPVHAVITNSTYDGLLYNTDFIKKTLDVKSIHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIYETQSTHKLLAAFSQASMIHVKGDVNEETFNEAYMMHTTTSPHYGIVASTETAAAMMKGNAGKRLINGSIERAIKFRKEIKRLRTESDGWFFDVWQPDHIDTTECWPLRSDSTWHGFKNIDNEHMYLDPIKVTLLTPGMEKDGTMSDFGIPASIVAKYLDEHGIVVEKTGPYNLLFLFSIGIDKTKALSLLRALTDFKRAFDLNLRVKNMLPSLYREDPEFYENMRIQELAQNIHKLIVHHNLPDLMYRAFEVLPTMVMTPYAAFQKELHGMTEEVYLDEMVGRINANMILPYPPGVPLVMPGEMITEESRPVLEFLQMLCEIGAHYPGFETDIHGAYRQADGRYTVKVLKEESKK DIP protein P0A9H3 original sequence version: 58 This sequence has been withdrawn from Uniprot. B9776622A0AE0190 cada-1 3 LdcI 6 predetermined predetermined participant predetermined predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified Stoichiometry: 2.0 direct interaction direct interaction mint The primary unit of the LdcI structure is the two-fold symmetric dimer (Figure 1B) within which the core domains of each monomer are tightly associated, while the wing domains project outwards from the body of the dimer...The LdcI decamer is B183A° wide and 93A° high and has a central pore of 25A° diameter as well as five 9A° wide side pores (Figure 2A). The decamer is formed by the association of five dimers to form a double-ringed structure with distinct five-fold symmetry. The structure determination of apo-LdcI is deposited in the RCSB with PDB ID 3N75 t1 f1b sf1 f2a f2d cada-1 2 LdcI 6 predetermined predetermined participant predetermined predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified Stoichiometry: 2.0 direct interaction direct interaction mint f2b sf7c f5b In the current work, we obtained an B20A° cryoEM reconstruction of LdcI (Figure 2B) that also clearly shows the central and side pores in the decameric structure...Class averages of the LdcI dimers in solution show that the overall conformation of the dimers closely matches the conformation that we determined in the crystal structure (Supplementary Figure S7C). This suggests that dimers free in solution maintain a conformation that favours decamer formation. cada-1 1 LdcI 6 predetermined predetermined participant predetermined predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified P0A9H3:p.Leu89Arg mutation decreasing interaction mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain L R Tue Jul 12 10:13:27 BST 2016 This feature has been corrected as a result of our quality control procedures. The original label was 'mutation decreasing' Wed May 02 17:01:43 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'leu89arg' Tue Jun 30 17:33:42 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Leu89Arg' Stoichiometry: 10.0 direct interaction direct interaction mint f5a f5d f6a At pH 5.0, large aggregates that elute in the void volume of the column were observed (exclusion limit of the column is B40 000 kDa) while at pH 6.5 and 8.0 decamers were dominant (Figure 5A)...The SEC profile of 20 mM LdcI (Figure 5D) shows that at pH 5.0, a range of large oligomeric species are present and that addition...The oligomerisation of the different mutants was tested by SEC at pH 6.5 (Figure 6A). The ppGpp-binding site mutants R97A and R206S showed wild-type oligomerisation profiles while L89R eluted at the expected position for an LdcI dimer (about 150 kDa). of 100 mM ppGpp shifts the distribution towards more decamers, consistent with the EM observations at lower enzyme concentrations (Figure 5B). cada-1 4 LdcI 6 predetermined predetermined participant predetermined predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified Stoichiometry: 10.0 direct interaction direct interaction mint sf7a Sedimentation velocity analytical ultracentrifugation experiments of 25 mM LdcI at pH 8.0 yielded similar results, while experiments at pH 6.5 showed a mixture of LdcI decamers and larger species (Supplementary Figure S7A). cada-1 5 LdcI 6 weight by staining molecular weight estimation by staining weight by staining predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified Stoichiometry: 10.0 direct interaction direct interaction mint sf7b