5dfr: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="5dfr" size="450" color="white" frame="true" align="right" spinBox="true" caption="5dfr, resolution 2.3Å" /> '''CRYSTAL STRUCTURE OF ...
 
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:5dfr.gif|left|200px]]<br /><applet load="5dfr" size="450" color="white" frame="true" align="right" spinBox="true"
caption="5dfr, resolution 2.3&Aring;" />
'''CRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. LIGAND-INDUCED CONFORMATIONAL CHANGES AND COOPERATIVITY IN BINDING'''<br />


==Overview==
==CRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. LIGAND-INDUCED CONFORMATIONAL CHANGES AND COOPERATIVITY IN BINDING==
The crystal structure of unliganded dihydrofolate reductase (DHFR) from, Escherichia coli has been solved and refined to an R factor of 19% at, 2.3-A resolution in a crystal form that is nonisomorphous with each of the, previously reported E. coli DHFR crystal structures [Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, B. C., &amp; Kraut, J. (1982) J. Biol. Chem., 257, 13650-13662; Bystroff, C., Oatley, S. J., &amp; Kraut, J. (1990), Biochemistry 29, 3263-3277]. Significant conformational changes occur, between the apoenzyme and each of the complexes: the NADP+ holoenzyme, the, folate-NADP+ ternary complex, and the methotrexate (MTX) binary complex., The changes are small, with the largest about 3 A and most of them less, than 1 A. For simplicity a two-domain description is adopted in which one, domain contains the NADP+ 2'-phosphate binding site and the binding sites, for the rest of the coenzyme and for the substrate lie between the two, domains. Binding of either NADP+ or MTX induces a closing of the, PABG-binding cleft and realignment of alpha-helices C and F which bind the, pyrophosphate of the coenzyme. Formation of the ternary complex from the, holoenzyme does not involve further relative domain shifts but does, involve a shift of alpha-helix B and a floppy loop (the Met-20 loop) that, precedes alpha B. These observations suggest a mechanism for cooperativity, in binding between substrate and coenzyme wherein the greatest degree of, cooperativity is expressed in the transition-state complex. We explore the, idea that the MTX binary complex in some ways resembles the, transition-state complex.
<StructureSection load='5dfr' size='340' side='right'caption='[[5dfr]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5dfr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DFR FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=5dfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dfr OCA], [https://pdbe.org/5dfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dfr RCSB], [https://www.ebi.ac.uk/pdbsum/5dfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dfr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/5dfr_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=5dfr ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
5DFR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with CL as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=5DFR OCA].
*[[Dihydrofolate reductase 3D structures|Dihydrofolate reductase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding., Bystroff C, Kraut J, Biochemistry. 1991 Feb 26;30(8):2227-39. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1998681 1998681]
[[Category: Dihydrofolate reductase]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Bystroff, C.]]
[[Category: Bystroff C]]
[[Category: Kraut, J.]]
[[Category: Kraut J]]
[[Category: CL]]
[[Category: oxido-reductase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:29:04 2007''

Latest revision as of 15:24, 6 March 2024

CRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. LIGAND-INDUCED CONFORMATIONAL CHANGES AND COOPERATIVITY IN BINDINGCRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. LIGAND-INDUCED CONFORMATIONAL CHANGES AND COOPERATIVITY IN BINDING

Structural highlights

5dfr is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DYR_ECOLI Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.

Evolutionary Conservation

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

See Also

5dfr, resolution 2.30Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=5dfr&oldid=4080453"