2j5k

From Proteopedia

(Difference between revisions)

Current revision

2.0 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui (radiation damage series)

Structural highlights

2j5k is a 4 chain structure with sequence from Haloarcula marismortui. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MDH_HALMA Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]

Evolutionary Conservation

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

Publication Abstract from PubMed

Intense synchrotron radiation produces specific structural and chemical damage to crystalline proteins even at 100 K. Carboxyl groups of acidic residues (Glu, Asp) losing their definition is one of the major effects observed. Here, the susceptibilities to X-ray damage of acidic residues in tetrameric malate dehydrogenase from Haloarcula marismortui are investigated. The marked excess of acidic residues in this halophilic enzyme makes it an ideal target to determine how specific damage to acidic residues is related to their structural and chemical environment. Four conclusions are drawn. (i) Acidic residues interacting with the side-chains of lysine and arginine residues are less affected by radiation damage than those interacting with serine, threonine and tyrosine side-chains. This suggests that residues with higher pK(a) values are more vulnerable to damage than those with a lower pK(a). However, such a correlation was not found when calculated pK(a) values were inspected. (ii) Acidic side-chains located in the enzymatic active site are the most radiation-sensitive ones. (iii) Acidic residues in the internal cavity formed by the four monomers and those involved in crystal contacts appear to be particularly susceptible. (iv) No correlation was found between radiation susceptibility and solvent accessibility.

Specific radiation damage to acidic residues and its relation to their chemical and structural environment.,Fioravanti E, Vellieux FM, Amara P, Madern D, Weik M J Synchrotron Radiat. 2007 Jan;14(Pt 1):84-91. Epub 2006 Dec 15. PMID:17211074^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Fioravanti E, Vellieux FM, Amara P, Madern D, Weik M. Specific radiation damage to acidic residues and its relation to their chemical and structural environment. J Synchrotron Radiat. 2007 Jan;14(Pt 1):84-91. Epub 2006 Dec 15. PMID:17211074 doi:10.1107/S0909049506038623

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2j5k"

@@ Line 1: / Line 1: @@
-==2.0 A RESOLUTION STRUCTURE OF THE WILD TYPE MALATE DEHYDROGENASE FROM HALOARCULA MARISMORTUI (RADIATION DAMAGE SERIES)==
-<StructureSection load='2j5k' size='340' side='right' caption='[[2j5k]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+==2.0 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui (radiation damage series)==
+<StructureSection load='2j5k' size='340' side='right'caption='[[2j5k]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2j5k]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_(halobacterium)_maris-mortui_(sic)"_elazari-volcani_1940 "flavobacterium (halobacterium) maris-mortui (sic)" elazari-volcani 1940]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2J5K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2j5k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J5K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
+</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1d3a|1d3a]], [[1gt2|1gt2]], [[1hlp|1hlp]], [[1o6z|1o6z]], [[2hlp|2hlp]], [[2j5q|2j5q]], [[2j5r|2j5r]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] </span></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=2j5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j5k OCA], [https://pdbe.org/2j5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j5k RCSB], [https://www.ebi.ac.uk/pdbsum/2j5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j5k ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j5k OCA], [http://pdbe.org/2j5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j5k RCSB], [http://www.ebi.ac.uk/pdbsum/2j5k PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MDH_HALMA MDH_HALMA]] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]
+[https://www.uniprot.org/uniprot/MDH_HALMA MDH_HALMA] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]
 == 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/j5/2j5k_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j5/2j5k_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2j5k ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Malate dehydrogenase|Malate dehydrogenase]]
+*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Malate dehydrogenase]]
+[[Category: Haloarcula marismortui]]
-[[Category: Amara, P]]
+[[Category: Large Structures]]
-[[Category: Fioravanti, E]]
+[[Category: Amara P]]
-[[Category: Madern, D]]
+[[Category: Fioravanti E]]
-[[Category: Vellieux, F M.D]]
+[[Category: Madern D]]
-[[Category: Weik, M]]
+[[Category: Vellieux FMD]]
-[[Category: Halophile]]
+[[Category: Weik M]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]
-[[Category: Radiation damage]]
-[[Category: Tricarboxylic acid cycle]]

2j5k

From Proteopedia

Current revision

2.0 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui (radiation damage series)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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