1b49

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1b49" size="450" color="white" frame="true" align="right" spinBox="true" caption="1b49, resolution 2.30&Aring;" /> '''DCMP HYDROXYMETHYLAS...)
Current revision (06:34, 7 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1b49.gif|left|200px]]<br /><applet load="1b49" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1b49, resolution 2.30&Aring;" />
 
-
'''DCMP HYDROXYMETHYLASE FROM T4 (PHOSPHATE-BOUND)'''<br />
 
-
==Overview==
+
==DCMP HYDROXYMETHYLASE FROM T4 (PHOSPHATE-BOUND)==
-
Bacteriophage T4 deoxycytidylate hydroxymethylase (EC 2.1.2.8), a, homodimer of 246-residue subunits, catalyzes hydroxymethylation of the, cytosine base in deoxycytidylate (dCMP) to produce 5-hydroxymethyl-dCMP., It forms part of a phage DNA protection system and appears to function in, vivo as a component of a multienzyme complex called deoxyribonucleoside, triphosphate (dNTP) synthetase. We have determined its crystal structure, in the presence of the substrate dCMP at 1.6 A resolution. The structure, reveals a subunit fold and a dimerization pattern in common with, thymidylate synthases, despite low (approximately 20%) sequence identity., Among the residues that form the dCMP binding site, those interacting with, the sugar and phosphate are arranged in a configuration similar to the, deoxyuridylate binding site of thymidylate synthases. However, the, residues interacting directly or indirectly with the cytosine base show a, more divergent structure and the presumed folate cofactor binding site is, more open. Our structure reveals a water molecule properly positioned near, C-6 of cytosine to add to the C-7 methylene intermediate during the last, step of hydroxymethylation. On the basis of sequence comparison and, crystal packing analysis, a hypothetical model for the interaction between, T4 deoxycytidylate hydroxymethylase and T4 thymidylate synthase in the, dNTP-synthesizing complex has been built.
+
<StructureSection load='1b49' size='340' side='right'caption='[[1b49]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1b49]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B49 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B49 FirstGlance]. <br>
-
1B49 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with PO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Deoxycytidylate_5-hydroxymethyltransferase Deoxycytidylate 5-hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.8 2.1.2.8] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1B49 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]] 2.3&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b49 OCA], [https://pdbe.org/1b49 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b49 RCSB], [https://www.ebi.ac.uk/pdbsum/1b49 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b49 ProSAT]</span></td></tr>
-
Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex., Song HK, Sohn SH, Suh SW, EMBO J. 1999 Mar 1;18(5):1104-13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10064578 10064578]
+
</table>
-
[[Category: Bacteriophage t4]]
+
== Function ==
-
[[Category: Deoxycytidylate 5-hydroxymethyltransferase]]
+
[https://www.uniprot.org/uniprot/DCHM_BPT4 DCHM_BPT4]
-
[[Category: Single protein]]
+
== Evolutionary Conservation ==
-
[[Category: Sohn, S.H.]]
+
[[Image:Consurf_key_small.gif|200px|right]]
-
[[Category: Song, H.K.]]
+
Check<jmol>
-
[[Category: Suh, S.W.]]
+
<jmolCheckbox>
-
[[Category: PO4]]
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/1b49_consurf.spt"</scriptWhenChecked>
-
[[Category: dntp synthesizing complex]]
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
[[Category: hydroxymethylase]]
+
<text>to colour the structure by Evolutionary Conservation</text>
-
 
+
</jmolCheckbox>
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:20:44 2007''
+
</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=1b49 ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Escherichia virus T4]]
 +
[[Category: Large Structures]]
 +
[[Category: Sohn SH]]
 +
[[Category: Song HK]]
 +
[[Category: Suh SW]]

Current revision

DCMP HYDROXYMETHYLASE FROM T4 (PHOSPHATE-BOUND)

PDB ID 1b49

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/1b49"
Personal tools