4kde: Difference between revisions
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The | ==Crystal Structure of the Apo Form of Thermus thermophilus Malate Dehydrogenase== | ||
<StructureSection load='4kde' size='340' side='right'caption='[[4kde]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4kde]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KDE FirstGlance]. <br> | |||
</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=4kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kde OCA], [https://pdbe.org/4kde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kde RCSB], [https://www.ebi.ac.uk/pdbsum/4kde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kde ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/MDH_THETH MDH_THETH] Catalyzes the reversible oxidation of malate to oxaloacetate. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Malate dehydrogenase (MDH) catalyzes the conversion of oxaloacetate and malate by using the NAD/NADH coenzyme system. The system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. We elucidated the biochemical and structural features of MDH from Thermus thermophilus (TtMDH) for use in various biotechnological applications. The biochemical characterization of recombinant TtMDH revealed greatly increased activity above 60 degrees C and specific activity of about 2,600 U/mg with optimal temperature of 90 degrees C. Analysis of crystal structures of apo and NAD-bound forms of TtMDH revealed a slight movement of the binding loop and few structural elements around the co-substrate binding packet in the presence of NAD. The overall structures did not change much and retained all related positions, which agrees with the CD analyses. Further molecular dynamics (MD) simulation at higher temperatures were used to reconstruct structures from the crystal structure of TtMDH. Interestingly, at the simulated structure of 353 K, a large change occurred around the active site such that with increasing temperature, a mobile loop was closed to co-substrate binding region. From biochemical characterization, structural comparison and MD simulations, the thermal-induced conformational change of the co-substrate binding loop of TtMDH may contribute to the essential movement of the enzyme for admitting NAD and may benefit the enzyme's activity. | |||
Crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding.,Hung CH, Hwang TS, Chang YY, Luo HR, Wu SP, Hsu CH PLoS One. 2013 Dec 26;8(12):e83091. doi: 10.1371/journal.pone.0083091., eCollection 2013. PMID:24386145<ref>PMID:24386145</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4kde" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thermus thermophilus]] | |||
[[Category: Chang Y-Y]] | |||
[[Category: Hong C-H]] | |||
[[Category: Hsu C-H]] | |||
Latest revision as of 14:53, 30 November 2022
Crystal Structure of the Apo Form of Thermus thermophilus Malate DehydrogenaseCrystal Structure of the Apo Form of Thermus thermophilus Malate Dehydrogenase
Structural highlights
FunctionMDH_THETH Catalyzes the reversible oxidation of malate to oxaloacetate. Publication Abstract from PubMedMalate dehydrogenase (MDH) catalyzes the conversion of oxaloacetate and malate by using the NAD/NADH coenzyme system. The system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. We elucidated the biochemical and structural features of MDH from Thermus thermophilus (TtMDH) for use in various biotechnological applications. The biochemical characterization of recombinant TtMDH revealed greatly increased activity above 60 degrees C and specific activity of about 2,600 U/mg with optimal temperature of 90 degrees C. Analysis of crystal structures of apo and NAD-bound forms of TtMDH revealed a slight movement of the binding loop and few structural elements around the co-substrate binding packet in the presence of NAD. The overall structures did not change much and retained all related positions, which agrees with the CD analyses. Further molecular dynamics (MD) simulation at higher temperatures were used to reconstruct structures from the crystal structure of TtMDH. Interestingly, at the simulated structure of 353 K, a large change occurred around the active site such that with increasing temperature, a mobile loop was closed to co-substrate binding region. From biochemical characterization, structural comparison and MD simulations, the thermal-induced conformational change of the co-substrate binding loop of TtMDH may contribute to the essential movement of the enzyme for admitting NAD and may benefit the enzyme's activity. Crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding.,Hung CH, Hwang TS, Chang YY, Luo HR, Wu SP, Hsu CH PLoS One. 2013 Dec 26;8(12):e83091. doi: 10.1371/journal.pone.0083091., eCollection 2013. PMID:24386145[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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