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5xd9

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Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase

Structural highlights

5xd9 is a 1 chain structure with sequence from Vibrio sp. EJY3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ACI_VIBSJ Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae. Catalyzes the isomerization of 3,6-anhydrogalactonate (AHGA) to 2-keto-3-deoxy-galactonate (KDGal).^[1]

Publication Abstract from PubMed

3,6-Anydro-l-galatonate cycloisomerase (ACI) catalyzes the cycloisomerization of a 3,6-anhydro-l-galactonic acid known as a novel metabolite in agarolytic bacteria. Here, we present 3-D structures of ACI from Vibrio sp. strain EJY3 (VejACI) in native and mutant forms at 2.2 A and 2.6 A resolutions, respectively. The enzyme belongs to the mandelate racemase subgroup of the enolase superfamily catalyzing common beta-elimination reactions by alpha-carbon deprotonation of substrates. The structure of VejACI revealed a notable 20s loop region in the capping domain, which can be a highly conserved structural motif in ACI homologs of agar metabolism. By comparing mutant (mVejAC/H300 N) and native VejACI structures, we identified a conformational change of Ile142 in VejACI that causes spatial expansion in the binding pocket. These observations imply that Ile142 and the 20s loop play important roles in enzymatic reactivity and substrate specificity. The structural phylogenetic analysis of the enolase superfamily including ACIs revealed sequential, structural, and functional relationships related to the emergence of novel substrate specificity.

Crystal structure analysis of 3,6-anhydro-l-galactonate cycloisomerase suggests emergence of novel substrate specificity in the enolase superfamily.,Lee S, Kim KH, Kim HY, Choi IG Biochem Biophys Res Commun. 2017 Sep 9;491(1):217-222. doi:, 10.1016/j.bbrc.2017.07.080. Epub 2017 Jul 14. PMID:28716734^[2]

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

References

↑ Yun EJ, Lee S, Kim HT, Pelton JG, Kim S, Ko HJ, Choi IG, Kim KH. The novel catabolic pathway of 3,6-anhydro-L-galactose, the main component of red macroalgae, in a marine bacterium. Environ Microbiol. 2015 May;17(5):1677-88. doi: 10.1111/1462-2920.12607. Epub, 2014 Sep 29. PMID:25156229 doi:http://dx.doi.org/10.1111/1462-2920.12607
↑ Lee S, Kim KH, Kim HY, Choi IG. Crystal structure analysis of 3,6-anhydro-l-galactonate cycloisomerase suggests emergence of novel substrate specificity in the enolase superfamily. Biochem Biophys Res Commun. 2017 Sep 9;491(1):217-222. doi:, 10.1016/j.bbrc.2017.07.080. Epub 2017 Jul 14. PMID:28716734 doi:http://dx.doi.org/10.1016/j.bbrc.2017.07.080

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/5xd9"

Categories: Large Structures | Vibrio sp. EJY3 | Choi I-G | Kim H-Y | Lee S

@@ Line 1: / Line 1: @@
 ==Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase==
-<StructureSection load='5xd9' size='340' side='right' caption='[[5xd9]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='5xd9' size='340' side='right'caption='[[5xd9]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5xd9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XD9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xd9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_sp._EJY3 Vibrio sp. EJY3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XD9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xd7|5xd7]], [[5xd8|5xd8]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isomerase Isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.5.1.25 5.5.1.25] </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=5xd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xd9 OCA], [https://pdbe.org/5xd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xd9 RCSB], [https://www.ebi.ac.uk/pdbsum/5xd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xd9 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5xd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xd9 OCA], [http://pdbe.org/5xd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xd9 RCSB], [http://www.ebi.ac.uk/pdbsum/5xd9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xd9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ACI_VIBSJ ACI_VIBSJ]] Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae. Catalyzes the isomerization of 3,6-anhydrogalactonate (AHGA) to 2-keto-3-deoxy-galactonate (KDGal).<ref>PMID:25156229</ref>
+[https://www.uniprot.org/uniprot/ACI_VIBSJ ACI_VIBSJ] Involved in the degradation of 3,6-anhydro-L-galactose, which is the major monomeric sugar of red macroalgae. Catalyzes the isomerization of 3,6-anhydrogalactonate (AHGA) to 2-keto-3-deoxy-galactonate (KDGal).<ref>PMID:25156229</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Isomerase]]
+[[Category: Large Structures]]
-[[Category: Choi, I G]]
+[[Category: Vibrio sp. EJY3]]
-[[Category: Kim, H Y]]
+[[Category: Choi I-G]]
-[[Category: Lee, S]]
+[[Category: Kim H-Y]]
-[[Category: 6-anhydro-l-galactonate cycloisomerase]]
+[[Category: Lee S]]
-[[Category: Barrel domain]]
-[[Category: Capping domain]]
-[[Category: Enolase superfamily]]
-[[Category: Lyase]]

5xd9

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Current revision

Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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