1d3a: Difference between revisions

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<StructureSection load='1d3a' size='340' side='right'caption='[[1d3a]], [[Resolution|resolution]] 2.94&Aring;' scene=''>
<StructureSection load='1d3a' size='340' side='right'caption='[[1d3a]], [[Resolution|resolution]] 2.94&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1d3a]] is a 2 chain structure with sequence from [https://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=1D3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3A FirstGlance]. <br>
<table><tr><td colspan='2'>[[1d3a]] is a 2 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=1D3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3A FirstGlance]. <br>
</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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.94&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2hlp|2hlp]]</div></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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [https://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=1d3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3a OCA], [https://pdbe.org/1d3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3a RCSB], [https://www.ebi.ac.uk/pdbsum/1d3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3a ProSAT]</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=1d3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3a OCA], [https://pdbe.org/1d3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3a RCSB], [https://www.ebi.ac.uk/pdbsum/1d3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3a ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1d3a 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=1d3a ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Previous biophysical studies of tetrameric malate dehydrogenase from the halophilic archaeon Haloarcula marismortui (Hm MalDH) have revealed the importance of protein-solvent interactions for its adaptation to molar salt conditions that strongly affect protein solubility, stability, and activity, in general. The structures of the E267R stability mutant of apo (-NADH) Hm MalDH determined to 2.6 A resolution and of apo (-NADH) wild type Hm MalDH determined to 2.9 A resolution, presented here, highlight a variety of novel protein-solvent features involved in halophilic adaptation. The tetramer appears to be stabilized by ordered water molecule networks and intersubunit complex salt bridges "locked" in by bound solvent chloride and sodium ions. The E267R mutation points into a central ordered water cavity, disrupting protein-solvent interactions. The analysis of the crystal structures showed that halophilic adaptation is not aimed uniquely at "protecting" the enzyme from the extreme salt conditions, as may have been expected, but, on the contrary, consists of mechanisms that harness the high ionic concentration in the environment.
Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 A resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui.,Richard SB, Madern D, Garcin E, Zaccai G Biochemistry. 2000 Feb 8;39(5):992-1000. PMID:10653643<ref>PMID:10653643</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1d3a" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]]
*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Haloarcula marismortui]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Malate dehydrogenase]]
[[Category: Garcin E]]
[[Category: Garcin, E]]
[[Category: Madern D]]
[[Category: Madern, D]]
[[Category: Richard SB]]
[[Category: Richard, S B]]
[[Category: Zaccai G]]
[[Category: Zaccai, G]]
[[Category: Oxidoreductase]]
[[Category: Rossmann fold and 3 sorts of complex salt bridge]]

Latest revision as of 09:48, 7 February 2024

CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORMCRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM

Structural highlights

1d3a is a 2 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 2.94Å
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.

See Also

1d3a, resolution 2.94Å

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