1otp: Difference between revisions

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'''STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE'''<br />


==Overview==
==STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE==
Two new crystal forms of Escherichia coli thymidine phosphorylase (EC, 2.4.2.4) have been found; a monoclinic form (space group P21) and an, orthorhombic form (space group I222). These structures have been solved, and compared to the previously determined tetragonal form (space group, P43212). This comparison provides evidence of domain movement of the alpha, (residues 1 to 65, 163 to 193) and alpha/beta (residues 80 to 154, 197 to, 440) domains, which is thought to be critical for enzymatic activity by, closing the active site cleft. Three hinge regions apparently allow the, alpha and alpha/beta-domains to move relative to each other. The, monoclinic model is the most open of the three models while the tetragonal, model is the most closed. Phosphate binding induces formation of a, hydrogen bond between His119 and Gly208, which helps to order the 115 to, 120 loop that is disordered prior to phosphate binding. The formation of, this hydrogen bond also appears to play a key role in the domain movement., The alpha-domain moves as a rigid body, while the alpha/beta-domain has, some non-rigid body movement that is associated with the formation of the, His119-Gly208 hydrogen bond. The 8 A distance between the two substrates, reported for the tetragonal form indicates that it is probably not in an, active conformation. However, the structural data for these two new, crystal forms suggest that closing the interdomain cleft around the, substrates may generate a functional active site. Molecular modeling and, dynamics simulation techniques have been used to generate a hypothetical, closed conformation of the enzyme. Analysis of this model suggests several, residues of possible catalytic importance. The model explains observed, kinetic results and satisfies requirements for efficient enzyme catalysis, most notably through the exclusion of water from the enzyme's active site.
<StructureSection load='1otp' size='340' side='right'caption='[[1otp]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1otp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OTP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OTP FirstGlance]. <br>
1OTP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Thymidine_phosphorylase Thymidine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.4 2.4.2.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OTP OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
 
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1otp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1otp OCA], [https://pdbe.org/1otp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1otp RCSB], [https://www.ebi.ac.uk/pdbsum/1otp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1otp ProSAT]</span></td></tr>
==Reference==
</table>
Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase., Pugmire MJ, Cook WJ, Jasanoff A, Walter MR, Ealick SE, J Mol Biol. 1998 Aug 14;281(2):285-99. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9698549 9698549]
== Function ==
[[Category: Escherichia coli]]
[https://www.uniprot.org/uniprot/TYPH_ECOLI TYPH_ECOLI] The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis.
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Thymidine phosphorylase]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Cook, W.J.]]
Check<jmol>
[[Category: Ealick, S.E.]]
  <jmolCheckbox>
[[Category: Jasanoff, A.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ot/1otp_consurf.spt"</scriptWhenChecked>
[[Category: Pugmire, M.J.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Walter, M.R.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: domain movement]]
  </jmolCheckbox>
[[Category: glycosyltransferase]]
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1otp ConSurf].
[[Category: phosphorylase]]
<div style="clear:both"></div>
[[Category: pyrimidine metabolism]]
__TOC__
[[Category: salvage pathway]]
</StructureSection>
[[Category: transferase]]
[[Category: Escherichia coli K-12]]
 
[[Category: Large Structures]]
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:11:43 2007''
[[Category: Cook WJ]]
[[Category: Ealick SE]]
[[Category: Jasanoff A]]
[[Category: Pugmire MJ]]
[[Category: Walter MR]]

Latest revision as of 11:03, 14 February 2024

STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASESTRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE

Structural highlights

1otp is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TYPH_ECOLI The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1otp, resolution 2.80Å

Drag the structure with the mouse to rotate

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