2tdd: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2tdd.jpg|left|200px]]


{{Structure
==STRUCTURES OF THYMIDYLATE SYNTHASE WITH A C-TERMINAL DELETION: ROLE OF THE C-TERMINUS IN ALIGNMENT OF D/UMP AND CH2H4FOLATE==
|PDB= 2tdd |SIZE=350|CAPTION= <scene name='initialview01'>2tdd</scene>, resolution 2.7&Aring;
<StructureSection load='2tdd' size='340' side='right'caption='[[2tdd]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=THF:5-HYDROXYMETHYLENE-6-HYDROFOLIC+ACID'>THF</scene>, <scene name='pdbligand=UFP:5-FLUORO-2&#39;-DEOXYURIDINE-5&#39;-MONOPHOSPHATE'>UFP</scene>
<table><tr><td colspan='2'>[[2tdd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lacticaseibacillus_casei Lacticaseibacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2TDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2TDD FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THF:5-HYDROXYMETHYLENE-6-HYDROFOLIC+ACID'>THF</scene>, <scene name='pdbligand=UFP:5-FLUORO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>UFP</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2tdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2tdd OCA], [https://pdbe.org/2tdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2tdd RCSB], [https://www.ebi.ac.uk/pdbsum/2tdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2tdd ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2tdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2tdd OCA], [http://www.ebi.ac.uk/pdbsum/2tdd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2tdd RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/TYSY_LACCA TYSY_LACCA] Provides the sole de novo source of dTMP for DNA biosynthesis.
== 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/td/2tdd_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=2tdd ConSurf].
<div style="clear:both"></div>


'''STRUCTURES OF THYMIDYLATE SYNTHASE WITH A C-TERMINAL DELETION: ROLE OF THE C-TERMINUS IN ALIGNMENT OF D/UMP AND CH2H4FOLATE'''
==See Also==
 
*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Thymidylate synthase undergoes a major conformational change upon ligand binding, where the carboxyl terminus displays the largest movement (approximately 4 A). This movement from an "open" unliganded state to the "closed" complexed conformation plays a crucial role in the correct orientation of substrates and in product formation. The mutant lacking the C-terminal valine (V316Am) of the enzyme is inactive. X-ray crystal structures of V316Am and its complexes with dUMP, FdUMP, and both FdUMP and CH2H4folate are described. The structures show that ligands are bound within the active site, but in different modes than those in analogous, wild-type thymidylate synthase structures. The 2.7-A binary complex structures of V316Am with FdUMP and dUMP show that the pyrimidine and ribose moieties of the nucleotides are pivoted approximately 20 degrees around the 3'-hydroxyl compared to dUMP in the wild-type enzyme. The 2.7-A crystal structure of V316Am complexed with cofactor, CH2H4folate, and the substrate analog, FdUMP, shows these ligands bound in an open conformation similar to that of the unliganded enzyme. In this ternary complex, the imidazolidine ring of the cofactor is open and has reacted with water to form 5-HOCH2H4folate. 5-HOCH2H4folate is structural evidence for the 5-iminium ion intermediate, which is the proposed reactive form of CH2H4folate. The altered ligand binding modes observed in the three V316Am complex structures open new venues for the design of novel TS inhibitors.
[[Category: Lacticaseibacillus casei]]
 
[[Category: Large Structures]]
==About this Structure==
[[Category: Carreras CW]]
2TDD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_casei Lactobacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2TDD OCA].
[[Category: Chang LC]]
 
[[Category: Perry KM]]
==Reference==
[[Category: Santi DV]]
Structures of thymidylate synthase with a C-terminal deletion: role of the C-terminus in alignment of 2'-deoxyuridine 5'-monophosphate and 5,10-methylenetetrahydrofolate., Perry KM, Carreras CW, Chang LC, Santi DV, Stroud RM, Biochemistry. 1993 Jul 20;32(28):7116-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8343503 8343503]
[[Category: Stroud RM]]
[[Category: Lactobacillus casei]]
[[Category: Single protein]]
[[Category: Thymidylate synthase]]
[[Category: Carreras, C W.]]
[[Category: Chang, L C.]]
[[Category: Perry, K M.]]
[[Category: Santi, D V.]]
[[Category: Stroud, R M.]]
[[Category: transferase (methyltranferase)]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:03:33 2008''

Latest revision as of 09:24, 21 February 2024

STRUCTURES OF THYMIDYLATE SYNTHASE WITH A C-TERMINAL DELETION: ROLE OF THE C-TERMINUS IN ALIGNMENT OF D/UMP AND CH2H4FOLATE

2tdd, resolution 2.70Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=2tdd&oldid=4063307"