1rag: Difference between revisions

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CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY

OverviewOverview

The X-ray crystal structure of CTP-ligated T state aspartate transcarbamoylase has been refined to an R factor of 0.182 at 2.5 A resolution using the computer program X-PLOR. The structure contains 81 sites for solvent and has rms deviations from ideality in bond lengths and bond angles of 0.018 A and 3.722 degrees, respectively. The cytosine base of CTP interacts with the main chain carbonyl oxygens of rTyr-89 and rIle-12, the main chain NH of rIle-12, and the amino group of rLys-60. The ribose hydroxyls form polar contacts with the amino group of rLys-60, a carboxylate oxygen of rAsp-19, and the main chain carbonyl oxygen of rVal-9. The phosphate oxygens of CTP interact with the amino group of rLys-94, the hydroxyl of rThr-82, and an imidazole nitrogen of rHis-20. Recent mutagenesis experiments evaluated in parallel with the structure reported here indicate that alterations in the hydrogen bonding environment of the side chain of rAsn-111 may be responsible for the homotropic behavior of the pAR5 mutant of ATCase. The location of the first seven residues of the regulatory chain has been identified for the first time in a refined ATCase crystal structure, and the proximity of this portion of the regulatory chain to the allosteric site suggests a potential role for these residues in nucleotide binding to the enzyme. Finally, a series of amino acid side chain rearrangements leading from the R1 CTP allosteric to the R6 CTP allosteric site has been identified which may constitute the molecular mechanism of distinct CTP binding sites on ATCase.

About this StructureAbout this Structure

1RAG is a Protein complex structure of sequences from Escherichia coli with and as ligands. Active as Aspartate carbamoyltransferase, with EC number 2.1.3.2 Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 A resolution: implications for ATCase mutants and the mechanism of negative cooperativity., Kosman RP, Gouaux JE, Lipscomb WN, Proteins. 1993 Feb;15(2):147-76. PMID:8441751

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-[[Image:1rag.jpg|left|200px]]<br /><applet load="1rag" size="450" color="white" frame="true" align="right" spinBox="true"
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 '''CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY'''<br />
 ==Overview==
-The X-ray crystal structure of CTP-ligated T state aspartate, transcarbamoylase has been refined to an R factor of 0.182 at 2.5 A, resolution using the computer program X-PLOR. The structure contains 81, sites for solvent and has rms deviations from ideality in bond lengths and, bond angles of 0.018 A and 3.722 degrees, respectively. The cytosine base, of CTP interacts with the main chain carbonyl oxygens of rTyr-89 and, rIle-12, the main chain NH of rIle-12, and the amino group of rLys-60. The, ribose hydroxyls form polar contacts with the amino group of rLys-60, a, carboxylate oxygen of rAsp-19, and the main chain carbonyl oxygen of, rVal-9. The phosphate oxygens of CTP interact with the amino group of, rLys-94, the hydroxyl of rThr-82, and an imidazole nitrogen of rHis-20., Recent mutagenesis experiments evaluated in parallel with the structure, reported here indicate that alterations in the hydrogen bonding, environment of the side chain of rAsn-111 may be responsible for the, homotropic behavior of the pAR5 mutant of ATCase. The location of the, first seven residues of the regulatory chain has been identified for the, first time in a refined ATCase crystal structure, and the proximity of, this portion of the regulatory chain to the allosteric site suggests a, potential role for these residues in nucleotide binding to the enzyme., Finally, a series of amino acid side chain rearrangements leading from the, R1 CTP allosteric to the R6 CTP allosteric site has been identified which, may constitute the molecular mechanism of distinct CTP binding sites on, ATCase.
+The X-ray crystal structure of CTP-ligated T state aspartate transcarbamoylase has been refined to an R factor of 0.182 at 2.5 A resolution using the computer program X-PLOR. The structure contains 81 sites for solvent and has rms deviations from ideality in bond lengths and bond angles of 0.018 A and 3.722 degrees, respectively. The cytosine base of CTP interacts with the main chain carbonyl oxygens of rTyr-89 and rIle-12, the main chain NH of rIle-12, and the amino group of rLys-60. The ribose hydroxyls form polar contacts with the amino group of rLys-60, a carboxylate oxygen of rAsp-19, and the main chain carbonyl oxygen of rVal-9. The phosphate oxygens of CTP interact with the amino group of rLys-94, the hydroxyl of rThr-82, and an imidazole nitrogen of rHis-20. Recent mutagenesis experiments evaluated in parallel with the structure reported here indicate that alterations in the hydrogen bonding environment of the side chain of rAsn-111 may be responsible for the homotropic behavior of the pAR5 mutant of ATCase. The location of the first seven residues of the regulatory chain has been identified for the first time in a refined ATCase crystal structure, and the proximity of this portion of the regulatory chain to the allosteric site suggests a potential role for these residues in nucleotide binding to the enzyme. Finally, a series of amino acid side chain rearrangements leading from the R1 CTP allosteric to the R6 CTP allosteric site has been identified which may constitute the molecular mechanism of distinct CTP binding sites on ATCase.
 ==About this Structure==
-RAG is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN and CTP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aspartate_carbamoyltransferase Aspartate carbamoyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.2 2.1.3.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RAG OCA].
+RAG is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=CTP:'>CTP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aspartate_carbamoyltransferase Aspartate carbamoyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.2 2.1.3.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RAG OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Escherichia coli]]
 [[Category: Protein complex]]
-[[Category: Gouaux, J.E.]]
+[[Category: Gouaux, J E.]]
-[[Category: Kosman, R.P.]]
+[[Category: Kosman, R P.]]
-[[Category: Lipscomb, W.N.]]
+[[Category: Lipscomb, W N.]]
 [[Category: CTP]]
 [[Category: ZN]]
 [[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:24:11 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:48:46 2008''