4dfr: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:4dfr.gif|left|200px]]


<!--
==CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE==
The line below this paragraph, containing "STRUCTURE_4dfr", creates the "Structure Box" on the page.
<StructureSection load='4dfr' size='340' side='right'caption='[[4dfr]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[4dfr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_B Escherichia coli B]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2dfr 2dfr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DFR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MTX:METHOTREXATE'>MTX</scene></td></tr>
{{STRUCTURE_4dfr| PDB=4dfr |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfr OCA], [https://pdbe.org/4dfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dfr RCSB], [https://www.ebi.ac.uk/pdbsum/4dfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dfr 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/4dfr_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=4dfr ConSurf].
<div style="clear:both"></div>


'''CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE'''
==See Also==
 
*[[Dihydrofolate reductase 3D structures|Dihydrofolate reductase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
X-ray data have been extended to 1.7 A for a binary complex of Escherichia coli dihydrofolate reductase with methotrexate and a ternary complex of Lactobacillus casei dihydrofolate reductase with methotrexate and NADPH. Models for both structures have been refined to R factors of 0.15 and include parameters for fixed and liquid solvent. The two species of dihydrofolate reductase resemble one another even more closely than was thought to be the case prior to refinement. Several new structural features have also been discovered. Among them are a cis peptide linking Gly-97 and Gly-98 (L. Casei numbering) in both species, an alpha helix involving residues 43 through 50 in the E. coli enzyme, and the existence of what may be a specific hydration site on exposed alpha helices. Refinement has led to a revised description of the details of methotrexate binding. We now see that a fixed water molecule mediates the interaction between methotrexate's 2-amino group and Thr-116 (L. casei numbering) and that the inhibitor's 4-amino group makes two hydrogen bonds with the enzyme (instead of one). Other revisions are also discussed. A hypothetical model for substrate binding is proposed in which the pteridine ring is turned upside down while all protein and solvent atoms remain fixed. Asp-26 in this model is hydrogen bonded to the substrate's 2-amino group and to N3.
[[Category: Escherichia coli B]]
 
[[Category: Large Structures]]
==About this Structure==
[[Category: Bolin JT]]
4DFR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_b Escherichia coli b]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2dfr 2dfr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFR OCA].
[[Category: Filman DJ]]
 
[[Category: Kraut J]]
==Reference==
[[Category: Matthews DA]]
Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate., Bolin JT, Filman DJ, Matthews DA, Hamlin RC, Kraut J, J Biol Chem. 1982 Nov 25;257(22):13650-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6815178 6815178]
[[Category: Dihydrofolate reductase]]
[[Category: Escherichia coli b]]
[[Category: Single protein]]
[[Category: Bolin, J T.]]
[[Category: Filman, D J.]]
[[Category: Kraut, J.]]
[[Category: Matthews, D A.]]
[[Category: Oxido-reductase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 22:22:59 2008''

Latest revision as of 13:48, 1 March 2024

CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATECRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE

Structural highlights

4dfr is a 2 chain structure with sequence from Escherichia coli B. This structure supersedes the now removed PDB entry 2dfr. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
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

4dfr, resolution 1.70Å

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=4dfr&oldid=4072909"