This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2tdm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:24, 21 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2tdm.jpg|left|200px]]
 
-
{{Structure
+
==STRUCTURE OF THYMIDYLATE SYNTHASE==
-
|PDB= 2tdm |SIZE=350|CAPTION= <scene name='initialview01'>2tdm</scene>, resolution 2.55&Aring;
+
<StructureSection load='2tdm' size='340' side='right'caption='[[2tdm]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=CAT:Catalytic+CYS'>CAT</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=UMP:2&#39;-DEOXYURIDINE 5&#39;-MONOPHOSPHATE'>UMP</scene>
+
<table><tr><td colspan='2'>[[2tdm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lacticaseibacillus_casei Lacticaseibacillus casei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1tdm 1tdm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2TDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2TDM FirstGlance]. <br>
-
|ACTIVITY= [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]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</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=2tdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2tdm OCA], [https://pdbe.org/2tdm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2tdm RCSB], [https://www.ebi.ac.uk/pdbsum/2tdm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2tdm ProSAT]</span></td></tr>
 +
</table>
 +
== 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/2tdm_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=2tdm ConSurf].
 +
<div style="clear:both"></div>
-
'''STRUCTURE OF THYMIDYLATE SYNTHASE'''
+
==See Also==
-
 
+
*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Crystal structures of two crystal forms of the complex of Lactobacillus casei (TS) with its substrate dUMP have been solved and refined at 2.55 A resolution. The two crystal forms differ by approximately 5% in the c-axis length. The TS-dUMP complexes are symmetric dimers with dUMP bound equivalently in both active sites. dUMP is non-covalently bound in the same conformation as in ternary complexes of TS with dUMP and cofactor or cofactor analogs. The same hydrogen bonds are made between TS and substrate in the binary and ternary complexes. We have also determined the 2.36 A crystal structure of phosphate-bound L. casei TS. This structure has been refined to an R-factor of 19.3% with highly constrained geometry. Refinement has revealed the locations of all residues in the protein, including the disordered residues 90 to 119, which are part of an insert found only in the L. casei and Staphylococcus aureus transposon Tn4003 TS sequences. The 2.9 A multiple isomorphous replacement (MIR) structure of L. casei TS in a complex with its substrate dUMP has been refined to a crystallographic R-factor of 15.5%. Reducing agents were withheld from crystallization solutions during MIR structure determination to allow heavy-metal labeling of the cysteine residues. Therefore, the active-site cysteine residue in this structure is oxidized and the dUMP is found at half-occupancy in the active site. No significant conformational difference was found between the phosphate-bound and dUMP-bound structures. The TS-dUMP structures were better ordered than the phosphate-bound TS or the oxidized TS-dUMP, particularly Arg23, which is clearly hydrogen-bonded to the phosphate group of dUMP. A large and a small P6(1)22 crystal form are observed for both phosphate-bound and dUMP-bound L. casei TS. The small cell forms of the phosphate-bound and dUMP-bound enzyme are isomorphous, whereas the cell constants of the larger cell form change slightly when dUMP is bound (c = 240 A versus c = 243 A). For both liganded and unliganded enzyme, conversion from the small to the large crystal form sometimes occurs spontaneously, and the crystal packing changes at a single interface. Conversion may be the result of a small change in pH in the mother liquor surrounding the crystal. A single intermolecular contact between symmetry-related Asp287 residues is disrupted on going from the small to the large crystal form.
+
[[Category: Lacticaseibacillus casei]]
-
 
+
[[Category: Large Structures]]
-
==About this Structure==
+
[[Category: Finer-Moore J]]
-
2TDM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_casei Lactobacillus casei]. This structure supersedes the now removed PDB entry 1TDM. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2TDM OCA].
+
[[Category: Stroud RM]]
-
 
+
-
==Reference==
+
-
Refined structures of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei., Finer-Moore J, Fauman EB, Foster PG, Perry KM, Santi DV, Stroud RM, J Mol Biol. 1993 Aug 20;232(4):1101-16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8371269 8371269]
+
-
[[Category: Lactobacillus casei]]
+
-
[[Category: Single protein]]
+
-
[[Category: Thymidylate synthase]]
+
-
[[Category: Finer-Moore, J.]]
+
-
[[Category: Stroud, R M.]]
+
-
[[Category: UMP]]
+
-
[[Category: methyltransferase]]
+
-
[[Category: transferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 15:50:43 2008''
+

Current revision

STRUCTURE OF THYMIDYLATE SYNTHASE

PDB ID 2tdm

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2tdm"
Personal tools