Sandbox Reserved 1057
Bold text==Isocitrate Lyase from Mycobacterium tuberculosis==
Wild Type ProteinWild Type Protein
3-Bromopyruvate3-Bromopyruvate
3-Nitropropionate3-Nitropropionate
This is a default text for your page Sydney Pate/Sandbox 1. Click above on edit this page to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue. Structure The active site of isocitrate lyase consists of eight residues: Trp93, Cys191, His193, Ser315, Ser317, Asn313, Thr347, Leu348. Additionally, there are several other amino acid side chains present that form hydrogen bonding opportunities with isocitrate to catalyze the breakdown reaction to glyoxylate and succinate. Ser91, Gly92, Trp93, and Arg228 form hydrogen bonds with glyoxylate while Asn313, Glu295, Arg228, and Gly192 and Trp93, Thr347, Ser315, Ser317, and His193 form hydrogen bonding opportunities with the two carboxylates within succinate. [3] Additionally, a Mg2+ ion is needed for further electrostatic stabilization of the extreme negative charge on isocitrate. This Mg2+ hydrogen bonds to the carboxylate in glyoxylate and one of the carboxylates in succinate. The catalytic loop of isocitrate lyase consists of residues 185-196. The two most important are Cys191 and His193 as these form a charge relay strong enough to extract a proton from isocitrate. Poor electron density has been observed for residues His193 and Leu194 indicating that this loop is very flexible. [3] This data backs up the claim that that monomers of the protein are in a structural equilibria between the open and closed forms of the active site. In order for the catalytic loop to shift into the closed position necessary for catalysis, isocitrate must be within the binding pocket. The hydrogen bonding opportunities formed cause a ripple effect that shifts the catalytic loop into a closer position. [3] This shift also causes the C-terminal domain of the subunit (residues 411-428) to move into the former position of the catalytic loop. The C-terminal domain is stabilized by an electrostatic interaction with Lys189. This combined movement locks the active site residues into a proper orientation for lysis of a C-C bond within isocitrate. [3]
Function
DiseaseRelevanceThe thiol group on the conserved Cys191 gets deprotonated by His193 residue to make it a better nucleophile that will deprotonate the alcohol on isocitrate. Mg2+ is used to stabalize the electrostatic repulsion of two of the three negative charges of the carboxylates. The oxyanion resonates to break a C-C bond forming two products and to force a carbonyl into an oxyanion. On this second product, the oxyanion resonates to form two carboxylates that are stabalized by a Mg ion.
Structural highlightsThis is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
|
| ||||||||||
ReferencesReferences
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
- ↑ 3.0 3.1 3.2 3.3 3.4 Sharma, V.; Sharma, S.; Hoener zu Bentrup, K.; McKinney, J.; Russell, D.; et. al; Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Nat. Struct. Biol.. 2000. 7(8):663-668.
- ↑ Gould, T.; van de Langemheen, H.; Muñoz-Elías, E.; McKinney, D.; Sacchettini, J.; Dual role of isocitrate lyase 1 in the glyoxylate and methylcitrate cycles in Mycobacterium tuberculosis. Molecular Microbiology. 2006. 61(4):940-947. doi:10.1111/j.1365-2958.2006.05297.x.