Sanbox Reserved 684: Difference between revisions

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Matthew Heard, Nick Shimko, Michal Harel

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 ===='''Structure'''====
 OTC is a trimer. The monomer unit has a CP-binding domain and an amino acid-binding domain. Each of the two discrete substrate-binding domains (SBDs) have an α/β topology with a central β-pleated sheet embedded in flanking α-helices.
-The <scene name='Sandbox_Reserved_644/Active_site/3'>active sites</scene> are located at the interface between the protein monomers.<ref>http://en.wikipedia.org/wiki/Ornithine_transcarbamylase</ref>The crystal structure of human ornithine transcarbamylase (OTCase) complexed with carbamoyl phosphate (CP) and L-norvaline (NOR) has been determined to 1.9-A resolution. There are significant differences in the interactions of CP with the protein, compared with the interactions of the CP moiety of the bisubstrate analogue N-(phosphonoacetyl)-L-ornithine (PALO). The carbonyl plane of CP rotates about 60 degrees compared with the equivalent plane in PALO complexed with OTCase. This positions the side chain of NOR optimally to interact with the carbonyl carbon of CP. The mixed-anhydride oxygen of CP, which is analogous to the methylene group in PALO, interacts with the guanidinium group of Arg-92; the primary carbamoyl nitrogen interacts with the main-chain carbonyl oxygens of Cys-303 and Leu-304, the side chain carbonyl oxygen of Gln-171, and the side chain of Arg-330. The residues that interact with NOR are similar to the residues that interact with the ornithine (ORN) moiety of PALO. The side chain of NOR is well defined and close to the side chain of Cys-303 with the side chains of Leu-163, Leu-200, Met-268, and Pro-305 forming a hydrophobic wall. C-delta of NOR is close to the carbonyl oxygen of Leu-304 (3.56 A), S-gamma atom of Cys-303 (4.19 A), and carbonyl carbon of CP (3.28 A). Even though the N-epsilon atom of ornithine is absent in this structure, the side chain of NOR is positioned to enable the N-epsilon of ornithine to donate a hydrogen to the S-gamma atom of Cys-303 along the reaction pathway. Binding of CP and NOR promotes domain closure to the same degree as PALO, and the active site structure of CP-NOR-enzyme complex is similar to that of the PALO-enzyme complex. The structures of the active sites in the complexes of aspartate transcarbamylase (ATCase) with various substrates or inhibitors are similar to this OTCase structure, consistent with their common evolutionary origin.<ref>http://www.proteopedia.org/wiki/index.php/1c9y<r/ref>
+The <scene name='Sandbox_Reserved_644/Active_site/3'>active sites</scene> are located at the interface between the protein monomers.<ref>http://en.wikipedia.org/wiki/Ornithine_transcarbamylase</ref>The crystal structure of human ornithine transcarbamylase (OTCase) complexed with carbamoyl phosphate (CP) and L-norvaline (NOR) has been determined to 1.9-A resolution. There are significant differences in the interactions of CP with the protein, compared with the interactions of the CP moiety of the bisubstrate analogue N-(phosphonoacetyl)-L-ornithine (PALO). The carbonyl plane of CP rotates about 60 degrees compared with the equivalent plane in PALO complexed with OTCase. This positions the side chain of NOR optimally to interact with the carbonyl carbon of CP. The mixed-anhydride oxygen of CP, which is analogous to the methylene group in PALO, interacts with the guanidinium group of Arg-92; the primary carbamoyl nitrogen interacts with the main-chain carbonyl oxygens of Cys-303 and Leu-304, the side chain carbonyl oxygen of Gln-171, and the side chain of Arg-330. The residues that interact with NOR are similar to the residues that interact with the ornithine (ORN) moiety of PALO. The side chain of NOR is well defined and close to the side chain of Cys-303 with the side chains of Leu-163, Leu-200, Met-268, and Pro-305 forming a hydrophobic wall. C-delta of NOR is close to the carbonyl oxygen of Leu-304 (3.56 A), S-gamma atom of Cys-303 (4.19 A), and carbonyl carbon of CP (3.28 A). Even though the N-epsilon atom of ornithine is absent in this structure, the side chain of NOR is positioned to enable the N-epsilon of ornithine to donate a hydrogen to the S-gamma atom of Cys-303 along the reaction pathway. Binding of CP and NOR promotes domain closure to the same degree as PALO, and the active site structure of CP-NOR-enzyme complex is similar to that of the PALO-enzyme complex. The structures of the active sites in the complexes of aspartate transcarbamylase (ATCase) with various substrates or inhibitors are similar to this OTCase structure, consistent with their common evolutionary origin.<ref>http://www.proteopedia.org/wiki/index.php/1c9y</ref>
-===='''Mechanism'''====
-The side-chain amino group of Orn attacks the carbonyl carbon of CP nucleophilically, to form a tetrahedral transition state, found in the middle. A Charge rearrangement then releases Cit and Pi.
-N5-Phosphonoacetyl-l-ornithine (PALO, 1) is a bisubstrate transition-state analog which competitively inhibits ornithine transcarbamylase (OTC) in vitro.<ref>https://www.google.com/#hl=en&sugexp=les%3B&gs_nf=3&gs_mss=Ornithine%20transcarbamylase%20in&tok=0eueaC5bjGY4yeUuw3p3dg&pq=ornithine%20transcarbamylase&cp=37&gs_id=30d&xhr=t&q=Ornithine%20transcarbamylase%20inhibitors&pf=p&safe=off&tbo=d&sclient=psy-ab&oq=Ornithine+transcarbamylase+inhibitors&gs_l=&pbx=1&bav=on.2,or.r_gc.r_pw.r_qf.&fp=689574a48716d7d0&bpcl=38093640&biw=1152&bih=499</ref>
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 The side chain amino group of Orn attacks the carbonyl carbon of CP nucleophillically, to form a tetrahedral transition state. A charge rearrangement then realeases Cit and Pi.
-N5-Phosphonoacetyl-l-ornithine (PALO, 1) is a bisubstrate transition-state analog which competitively inhibits ornithine transcarbamylase (OTC) in vitro. Studies have also shown that N δ-(N′-sulfodiaminophosphinyl)-l-ornithine (PSOrn), with its three unique N-P bonds, represents a true transition state analogue for ornithine transcarbamoylases (OTC). Another inhibitor being studied is The inhibition of ornithine transcarbamoylase from Escherichia coli W by phaseolotoxin. In the presence of phaseolotoxin ornithine transcarbamoylase exhibited a transient phase of activity before a steady state.
+N5-Phosphonoacetyl-l-ornithine (PALO, 1) is a bisubstrate transition-state analog which competitively inhibits ornithine transcarbamylase (OTC) in vitro.<ref>http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CDMQFjAA&url=http%3A%2F%2Fdigitalcommons.unl.edu%2Fcgi%2Fviewcontent.cgi%3Farticle%3D1009%26context%3Dchemistrydussault&ei=00qkUPOCIYqs9ATd9YHwBQ&usg=AFQjCNH-HXNQ5-7yov_T0Z-TGxDhjGAXyQ</ref>Studies have also shown that N δ-(N′-sulfodiaminophosphinyl)-l-ornithine (PSOrn), with its three unique N-P bonds, represents a true transition state analogue for ornithine transcarbamoylases (OTC). Another inhibitor being studied is The inhibition of ornithine transcarbamoylase from Escherichia coli W by phaseolotoxin. In the presence of phaseolotoxin ornithine transcarbamoylase exhibited a transient phase of activity before a steady state.
+References: {{reflist}}