1a05

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1a05" size="450" color="white" frame="true" align="right" spinBox="true" caption="1a05, resolution 2.00&Aring;" /> '''CRYSTAL STRUCTURE OF...)
Current revision (10:42, 2 August 2023) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1a05.gif|left|200px]]<br /><applet load="1a05" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1a05, resolution 2.00&Aring;" />
 
-
'''CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE'''<br />
 
-
==Overview==
+
==CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE==
-
BACKGROUND: 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate, dehydrogenase (ICDH) belong to a unique family of bifunctional, decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its, reaction under a closed conformation, known structures of the IPMDH dimer, (without substrate) adopt a fully open or a partially closed form., Considering the similarity in the catalytic mechanism, the IPMDH dimer, must be in a fully closed conformation during the reaction. A large, conformational change should therefore occur upon substrate binding., RESULTS: We have determined the crystal structure of IPMDH from, Thiobacillus ferrooxidans (Tf) complexed with 3-isopropylmalate (IPM) at, 2.0 A resolution by the molecular replacement method. The structure shows, a fully closed conformation and the substrate-binding site is quite, similar to that of ICDH except for a region around the gamma-isopropyl, group. The gamma group is recognized by a unique hydrophobic pocket, which, includes Glu88, Leu91 and Leu92 from subunit 1 and Val193' from subunit 2., CONCLUSIONS: A large movement of domain 1 is induced by substrate binding, which results in the formation of the hydrophobic pocket for the, gamma-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The C beta and C, gamma atoms of Glu88 interact with the gamma-isopropyl moiety of IPM and, are central to the recognition of substrate. The acidic tip of Glu88 is, likely to interact with the nicotinamide mononucleotide (NMN) ribose of, NAD+ in the ternary complex. This structure clearly explains the substrate, specificity of IPMDH.
+
<StructureSection load='1a05' size='340' side='right'caption='[[1a05]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1a05]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidithiobacillus_ferrooxidans Acidithiobacillus ferrooxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A05 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&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPM:3-ISOPROPYLMALIC+ACID'>IPM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1a05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a05 OCA], [https://pdbe.org/1a05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a05 RCSB], [https://www.ebi.ac.uk/pdbsum/1a05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a05 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/LEU3_ACIFR LEU3_ACIFR] 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.
 +
== 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/a0/1a05_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=1a05 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
BACKGROUND: 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding. RESULTS: We have determined the crystal structure of IPMDH from Thiobacillus ferrooxidans (Tf) complexed with 3-isopropylmalate (IPM) at 2.0 A resolution by the molecular replacement method. The structure shows a fully closed conformation and the substrate-binding site is quite similar to that of ICDH except for a region around the gamma-isopropyl group. The gamma group is recognized by a unique hydrophobic pocket, which includes Glu88, Leu91 and Leu92 from subunit 1 and Val193' from subunit 2. CONCLUSIONS: A large movement of domain 1 is induced by substrate binding, which results in the formation of the hydrophobic pocket for the gamma-isopropyl moiety of IPM. A glutamic acid in domain 1, Glu88, participates in the formation of the hydrophobic pocket. The C beta and C gamma atoms of Glu88 interact with the gamma-isopropyl moiety of IPM and are central to the recognition of substrate. The acidic tip of Glu88 is likely to interact with the nicotinamide mononucleotide (NMN) ribose of NAD+ in the ternary complex. This structure clearly explains the substrate specificity of IPMDH.
-
==About this Structure==
+
Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism.,Imada K, Inagaki K, Matsunami H, Kawaguchi H, Tanaka H, Tanaka N, Namba K Structure. 1998 Aug 15;6(8):971-82. PMID:9739088<ref>PMID:9739088</ref>
-
1A05 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Acidithiobacillus_ferrooxidans Acidithiobacillus ferrooxidans] with MG and IPM as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1A05 OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism., Imada K, Inagaki K, Matsunami H, Kawaguchi H, Tanaka H, Tanaka N, Namba K, Structure. 1998 Aug 15;6(8):971-82. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9739088 9739088]
+
</div>
-
[[Category: 3-isopropylmalate dehydrogenase]]
+
<div class="pdbe-citations 1a05" style="background-color:#fffaf0;"></div>
-
[[Category: Acidithiobacillus ferrooxidans]]
+
-
[[Category: Single protein]]
+
-
[[Category: Imada, K.]]
+
-
[[Category: Inagaki, K.]]
+
-
[[Category: Kawaguchi, H.]]
+
-
[[Category: Matsunami, H.]]
+
-
[[Category: Namba, K.]]
+
-
[[Category: Tanaka, H.]]
+
-
[[Category: Tanaka, N.]]
+
-
[[Category: IPM]]
+
-
[[Category: MG]]
+
-
[[Category: decarboxylating dehydrogenase]]
+
-
[[Category: leucine biosynthesis]]
+
-
[[Category: oxidoreductase]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:31:37 2007''
+
==See Also==
 +
*[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Acidithiobacillus ferrooxidans]]
 +
[[Category: Large Structures]]
 +
[[Category: Imada K]]
 +
[[Category: Inagaki K]]
 +
[[Category: Kawaguchi H]]
 +
[[Category: Matsunami H]]
 +
[[Category: Namba K]]
 +
[[Category: Tanaka H]]
 +
[[Category: Tanaka N]]

Current revision

CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE

PDB ID 1a05

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1a05"
Personal tools