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4uxd

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2-keto 3-deoxygluconate aldolase from Picrophilus torridus

Structural highlights

4uxd is a 4 chain structure with sequence from Picrophilus torridus. 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

KDGA_PICTO Involved in the degradation of glucose via the Entner-Doudoroff pathway. Catalyzes the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxygluconate (KDG) forming pyruvate and glyceraldehyde 3-phosphate or glyceraldehyde, respectively. It is also able to catalyze the reversible cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) and 2-keto-3-deoxygalactonate (KDGal). It is equally active with both D- and L-glyceraldehyde.^[1]

Publication Abstract from PubMed

The thermoacidophilic archaea Picrophilus torridus and Sulfolobus solfataricus catabolize glucose via a nonphosphorylative Entner-Doudoroff pathway and a branched Entner-Doudoroff pathway, respectively. Key enzymes for these Entner-Doudoroff pathways are the aldolases, 2-keto-3-deoxygluconate aldolase (KDG-aldolase) and 2-keto-3-deoxy-6-phosphogluconate aldolase [KD(P)G-aldolase]. KDG-aldolase from P. torridus (Pt-KDG-aldolase) is highly specific for the nonphosphorylated substrate, 2-keto-3-deoxygluconate (KDG), whereas KD(P)G-aldolase from S. solfataricus [Ss-KD(P)G-aldolase] is an enzyme that catalyzes the cleavage of both KDG and 2-keto-3-deoxy-6-phosphogluconate (KDPG), with a preference for KDPG. The structural basis for the high specificity of Pt-KDG-aldolase for KDG as compared to the more promiscuous Ss-KD(P)G-aldolase has not been analyzed before. In this work, we report the elucidation of the structure of Ss-KD(P)G-aldolase in complex with KDPG at 2.35 A and that of KDG-aldolase from P. torridus at 2.50 A resolution. By superimposition of the active sites of the two enzymes, and subsequent site-directed mutagenesis studies, a network of four amino acids, namely, Arg106, Tyr132, Arg237, and Ser241, was identified in Ss-KD(P)G-aldolase that interact with the negatively charged phosphate group of KDPG, thereby increasing the affinity of the enzyme for KDPG. This KDPG-binding network is absent in Pt-KDG-aldolase, which explains the low catalytic efficiency of KDPG cleavage.

Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3-deoxy-6-phosphogluconate Aldolase in Complex with 2-Keto-3-deoxy-6-phosphogluconate.,Zaitsev V, Johnsen U, Reher M, Ortjohann M, Taylor GL, Danson MJ, Schonheit P, Crennell SJ Biochemistry. 2018 Jun 13. doi: 10.1021/acs.biochem.8b00535. PMID:29812914^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Reher M, Fuhrer T, Bott M, Schonheit P. The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase. J Bacteriol. 2010 Feb;192(4):964-74. doi: 10.1128/JB.01281-09. Epub 2009 Dec 18. PMID:20023024 doi:http://dx.doi.org/10.1128/JB.01281-09
↑ Zaitsev V, Johnsen U, Reher M, Ortjohann M, Taylor GL, Danson MJ, Schonheit P, Crennell SJ. Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3-deoxy-6-phosphogluconate Aldolase in Complex with 2-Keto-3-deoxy-6-phosphogluconate. Biochemistry. 2018 Jun 13. doi: 10.1021/acs.biochem.8b00535. PMID:29812914 doi:http://dx.doi.org/10.1021/acs.biochem.8b00535

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4uxd"

@@ Line 3: / Line 3: @@
 <StructureSection load='4uxd' size='340' side='right'caption='[[4uxd]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4uxd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700027 Atcc 700027]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4UXD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4uxd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Picrophilus_torridus Picrophilus torridus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UXD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.5&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4uxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxd OCA], [http://pdbe.org/4uxd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uxd RCSB], [http://www.ebi.ac.uk/pdbsum/4uxd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4uxd ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=4uxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uxd OCA], [https://pdbe.org/4uxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uxd RCSB], [https://www.ebi.ac.uk/pdbsum/4uxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uxd ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/KDGA_PICTO KDGA_PICTO] Involved in the degradation of glucose via the Entner-Doudoroff pathway. Catalyzes the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxygluconate (KDG) forming pyruvate and glyceraldehyde 3-phosphate or glyceraldehyde, respectively. It is also able to catalyze the reversible cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) and 2-keto-3-deoxygalactonate (KDGal). It is equally active with both D- and L-glyceraldehyde.<ref>PMID:20023024</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 700027]]
 [[Category: Large Structures]]
-[[Category: Crennell, S J]]
+[[Category: Picrophilus torridus]]
-[[Category: Danson, M J]]
+[[Category: Crennell SJ]]
-[[Category: Johnsen, U]]
+[[Category: Danson MJ]]
-[[Category: Priftis, A]]
+[[Category: Johnsen U]]
-[[Category: Reher, M]]
+[[Category: Priftis A]]
-[[Category: Schoenheit, P]]
+[[Category: Reher M]]
-[[Category: Taylor, G L]]
+[[Category: Schoenheit P]]
-[[Category: Zaitsev, V]]
+[[Category: Taylor GL]]
-[[Category: Lyase]]
+[[Category: Zaitsev V]]
-[[Category: Tim barrel]]

4uxd

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Current revision

2-keto 3-deoxygluconate aldolase from Picrophilus torridus

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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