This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5xd7

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

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

Structural highlights

5xd7 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 2.198Å
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/5xd7"

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='5xd7' size='340' side='right' caption='[[5xd7]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='5xd7' size='340' side='right'caption='[[5xd7]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5xd7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XD7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XD7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xd7]] 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=5XD7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XD7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <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]] 2.198&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xd8|5xd8]], [[5xd9|5xd9]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <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=5xd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xd7 OCA], [https://pdbe.org/5xd7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xd7 RCSB], [https://www.ebi.ac.uk/pdbsum/5xd7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xd7 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=5xd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xd7 OCA], [http://pdbe.org/5xd7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xd7 RCSB], [http://www.ebi.ac.uk/pdbsum/5xd7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xd7 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]]

5xd7

From Proteopedia

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?)

Views

Personal tools

Navigation

Search

Toolbox