1dv7: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(16 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1dv7.gif|left|200px]]<br /><applet load="1dv7" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1dv7, resolution 1.80&Aring;" />
'''CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE'''<br />


==Overview==
==CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE==
Orotidine 5'-monophosphate decarboxylase catalyzes the conversion of orotidine 5'-monophosphate to uridine 5'-monophosphate, the last step in biosynthesis of pyrimidine nucleotides. As part of a Structural Genomics Initiative, the crystal structures of the ligand-free and the6-azauridine 5'-monophosphate-complexed forms have been determined at 1.8 and 1.5 A, respectively. The protein assumes a TIM-barrel fold with one side of the barrel closed off and the other side binding the inhibitor. A unique array of alternating charges (Lys-Asp-Lys-Asp) in the active site prompted us to apply quantum mechanical and molecular dynamics calculations to analyze the relative contributions of ground state destabilization and transition state stabilization to catalysis. The remarkable catalytic power of orotidine 5'-monophosphate decarboxylase is almost exclusively achieved via destabilization of the reactive part of the substrate, which is compensated for by strong binding of the phosphate and ribose groups. The computational results are consistent with a catalytic mechanism that is characterized by Jencks's Circe effect.
<StructureSection load='1dv7' size='340' side='right'caption='[[1dv7]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1dv7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV7 FirstGlance]. <br>
1DV7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Active as [http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV7 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]] 1.8&#8491;</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=1dv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv7 OCA], [https://pdbe.org/1dv7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv7 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv7 ProSAT], [https://www.topsan.org/Proteins/NESGC/1dv7 TOPSAN]</span></td></tr>
==Reference==
</table>
Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase., Wu N, Mo Y, Gao J, Pai EF, Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2017-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10681441 10681441]
== Function ==
[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
== 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/dv/1dv7_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=1dv7 ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Orotidine-5'-phosphate decarboxylase]]
[[Category: Gao J]]
[[Category: Single protein]]
[[Category: Mo Y]]
[[Category: Gao, J.]]
[[Category: Pai EF]]
[[Category: Mo, Y.]]
[[Category: Wu N]]
[[Category: Pai, E F.]]
[[Category: Wu, N.]]
[[Category: dimer]]
[[Category: lyase]]
[[Category: tim barrel]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:20:51 2008''

Latest revision as of 09:59, 7 February 2024

CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASECRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE

Structural highlights

1dv7 is a 1 chain structure with sequence from Methanothermobacter thermautotrophicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

PYRF_METTH Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]

Evolutionary Conservation

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

1dv7, resolution 1.80Å

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=1dv7&oldid=4042323"