2d4a: Difference between revisions

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<StructureSection load='2d4a' size='340' side='right'caption='[[2d4a]], [[Resolution|resolution]] 2.87&Aring;' scene=''>
<StructureSection load='2d4a' size='340' side='right'caption='[[2d4a]], [[Resolution|resolution]] 2.87&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4A FirstGlance]. <br>
<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4A FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.87&#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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [https://pdbe.org/2d4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [https://www.ebi.ac.uk/pdbsum/2d4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4a 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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [https://pdbe.org/2d4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [https://www.ebi.ac.uk/pdbsum/2d4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4a ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/MDH_AERPE MDH_AERPE]] Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP.<ref>PMID:19555779</ref>
[https://www.uniprot.org/uniprot/MDH_AERPE MDH_AERPE] Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP.<ref>PMID:19555779</ref>  
== 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=2d4a 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=2d4a ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Tartrate oxidation activity was found in the crude extract of an aerobic hyperthermophilic archaeon Aeropyrum pernix, and the enzyme was identified as (S)-malate dehydrogenase (MDH), which, when produced in Escherichia coli, was mainly obtained as an inactive inclusion body. The inclusion body was dissolved in 6 M guanidine-HCl and gradually refolded to the active enzyme through dilution of the denaturant. The purified recombinant enzyme consisted of four identical subunits with a molecular mass of about 110 kDa. NADP was preferred as a coenzyme over NAD for (S)-malate oxidation and, unlike MDHs from other sources, this enzyme readily catalyzed the oxidation of (2S,3S)-tartrate and (2S,3R)-tartrate. The tartrate oxidation activity was also observed in MDHs from the hyperthermophilic archaea Methanocaldococcus jannaschii and Archaeoglobus fulgidus, suggesting these hyperthermophilic MDHs loosely bind their substrates. The refolded A. pernix MDH was also crystallized, and the structure was determined at a resolution of 2.9 A. Its overall structure was similar to those of the M. jannaschii, Chloroflexus aurantiacus, Chlorobium vibrioforme and Cryptosporidium parvum [lactate dehydrogenase-like] MDHs with root-mean-square-deviation values between 1.4 and 2.1 A. Consistent with earlier reports, Ala at position 53 was responsible for coenzyme specificity, and the next residue, Arg, was important for NADP binding. Structural comparison revealed that the hyperthermostability of the A. pernix MDH is likely attributable to its smaller cavity volume and larger numbers of ion pairs and ion-pair networks, but the molecular strategy for thermostability may be specific for each enzyme.
Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.,Kawakami R, Sakuraba H, Goda S, Tsuge H, Ohshima T Biochim Biophys Acta. 2009 Oct;1794(10):1496-504. Epub 2009 Jun 23. PMID:19555779<ref>PMID:19555779</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2d4a" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Aerpx]]
[[Category: Aeropyrum pernix]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Malate dehydrogenase]]
[[Category: Kawakami R]]
[[Category: Kawakami, R]]
[[Category: Ohshima T]]
[[Category: Ohshima, T]]
[[Category: Sakuraba H]]
[[Category: Sakuraba, H]]
[[Category: Tsuge H]]
[[Category: Tsuge, H]]
[[Category: Archaea]]
[[Category: Hyperthermophile]]
[[Category: Oxidoreductase]]

Latest revision as of 16:46, 13 March 2024

Structure of the malate dehydrogenase from Aeropyrum pernixStructure of the malate dehydrogenase from Aeropyrum pernix

Structural highlights

2d4a is a 4 chain structure with sequence from Aeropyrum pernix. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.87Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MDH_AERPE Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP.[1]

Evolutionary Conservation

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

See Also

References

  1. ↑ Kawakami R, Sakuraba H, Goda S, Tsuge H, Ohshima T. Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix. Biochim Biophys Acta. 2009 Oct;1794(10):1496-504. Epub 2009 Jun 23. PMID:19555779 doi:10.1016/j.bbapap.2009.06.014

2d4a, resolution 2.87Å

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