1hex: Difference between revisions

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New page: left|200px<br /><applet load="1hex" size="450" color="white" frame="true" align="right" spinBox="true" caption="1hex, resolution 2.5Å" /> '''STRUCTURE OF 3-ISOPRO...
 
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'''STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE IN COMPLEX WITH NAD+: LIGAND-INDUCED LOOP-CLOSING AND MECHANISM FOR COFACTOR SPECIFICITY'''<br />


==Overview==
==STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE IN COMPLEX WITH NAD+: LIGAND-INDUCED LOOP-CLOSING AND MECHANISM FOR COFACTOR SPECIFICITY==
BACKGROUND: The leucine biosynthetic enzyme 3-isopropylmalate, dehydrogenase (IMDH) belongs to a unique class of bifunctional, decarboxylating dehydrogenases. The two best-known members of this family, IMDH and isocitrate dehydrogenase (IDH), share a common structural, framework and catalytic mechanism but have different substrate and, cofactor specificities. IMDH is NAD(+)-dependent, while IDHs occur in both, NAD(+)-dependent and NADP(+)-dependent forms. RESULTS: We have, co-crystallized Thermus thermophilus IMDH with NAD+ and have determined, the structure at 2.5 A resolution. NAD+ binds in an extended conformation., Comparisons with the structure in the absence of cofactor show that, binding induces structural changes of up to 2.5 A in the five loops which, form the dinucleotide-binding site. The adenine and diphosphate moieties, of NAD+ are bound via interactions which are also present in the, NADP(+)-IDH complex. Amino acids which interact with the NADP+, 2'-phosphate in IDH are substituted or absent in IMDH. The adenosine, ribose forms two hydrogen bonds with Asp278, and the nicotinamide and, nicotinamide ribose interact with Glu87 and Asp78, all unique to IMDH., CONCLUSIONS: NAD+ binding induces a conformational transition in IMDH, resulting in a structure that is intermediate between the most 'open' and, 'closed' decarboxylating dehydrogenase conformations. Physiological, specificity of IMDH for NAD+ versus NADP+ can be explained by the unique, interaction between Asp278 and the free 2'-hydroxyl of the NAD+ adenosine, discrimination against the presence of the 2'-phosphate by the negative, charge on Asp278, and the absence of potential favorable interactions with, the 2'-phosphate of NADP+.
<StructureSection load='1hex' size='340' side='right'caption='[[1hex]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1hex]] is a 1 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=1HEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HEX FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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=1hex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hex OCA], [https://pdbe.org/1hex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hex RCSB], [https://www.ebi.ac.uk/pdbsum/1hex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hex ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/LEU3_THET8 LEU3_THET8] Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate.[HAMAP-Rule:MF_01033]
== 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/he/1hex_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=1hex ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1HEX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with NAD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/3-isopropylmalate_dehydrogenase 3-isopropylmalate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.85 1.1.1.85] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1HEX OCA].
*[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]]
 
__TOC__
==Reference==
</StructureSection>
Structure of 3-isopropylmalate dehydrogenase in complex with NAD+: ligand-induced loop closing and mechanism for cofactor specificity., Hurley JH, Dean AM, Structure. 1994 Nov 15;2(11):1007-16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7881901 7881901]
[[Category: Large Structures]]
[[Category: 3-isopropylmalate dehydrogenase]]
[[Category: Single protein]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: Hurley, J.H.]]
[[Category: Hurley JH]]
[[Category: NAD]]
[[Category: oxidoreductase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 16:33:36 2007''

Latest revision as of 10:27, 7 February 2024

STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE IN COMPLEX WITH NAD+: LIGAND-INDUCED LOOP-CLOSING AND MECHANISM FOR COFACTOR SPECIFICITYSTRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE IN COMPLEX WITH NAD+: LIGAND-INDUCED LOOP-CLOSING AND MECHANISM FOR COFACTOR SPECIFICITY

Structural highlights

1hex is a 1 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LEU3_THET8 Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate.[HAMAP-Rule:MF_01033]

Evolutionary Conservation

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

See Also

1hex, resolution 2.50Å

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