5xne

From Proteopedia

(Difference between revisions)

Current revision

X-ray Crystal Structure of alpha-acetolactate decarboxylase from Bacillus subtilis strain 168

Structural highlights

5xne is a 2 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.501Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ALDC_BACSU Converts acetolactate into acetoin, which can be excreted by the cells. This may be a mechanism for controlling the internal pH of cells in the stationary stage.

Publication Abstract from PubMed

Acetoin is an important physiological metabolite excreted by microbes. Its functions include avoiding acidification, participating in regulation of the NAD(+)/NADH ratio, and storing carbon. Acetolactate decarboxylase is a well-characterized anabolic enzyme involved with 3-hydroxy butanone (acetoin). It catalyzes conversion of the (R)- and (S)-enantiomers of acetolactate to generate the single product, (R)-acetoin. In addition to the X-ray crystal structure of acetolactate decarboxylase from Bacillus brevis, although the enzyme is widely present in microorganisms, very few atomic structures of acetolactate decarboxylase are reported. In this paper, we solved and reported a 1.5 A resolution crystal structure of acetolactate decarboxylase from Bacillus subtilis. Dimeric assembly is observed in the solved structure, which is consistent with the elution profile conducted by molecular filtration. A zinc ion is coordinated by highly conserved histidines (191, 193, and 204) and conserved glutamates (62 and 251). We performed kinetic studies on acetolactate decarboxylase from Bacillus subtilis using circular dichroism, allowing the conversion of acetolactate to chiral acetoin for real-time tracking, yielding a Km value of 21 mM and a kcat value of 2.2 s(-1). Using the two enantiomers of acetolactate as substrates, we further investigated the substrate preference of acetolactate decarboxylase from Bacillus subtilis by means of molecular docking and dynamic simulation in silico. The binding free energy of (S)-acetolactate was found to be ~ 30 kcal/mol greater than that of (R)-acetolactate, indicating a more stable binding for (S)-acetolactate.

Structural and enzymatic characterization of acetolactate decarboxylase from Bacillus subtilis.,Ji F, Li M, Feng Y, Wu S, Wang T, Pu Z, Wang J, Yang Y, Xue S, Bao Y Appl Microbiol Biotechnol. 2018 Aug;102(15):6479-6491. doi:, 10.1007/s00253-018-9049-7. Epub 2018 May 23. PMID:29796971^[1]

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

References

↑ Ji F, Li M, Feng Y, Wu S, Wang T, Pu Z, Wang J, Yang Y, Xue S, Bao Y. Structural and enzymatic characterization of acetolactate decarboxylase from Bacillus subtilis. Appl Microbiol Biotechnol. 2018 Aug;102(15):6479-6491. doi:, 10.1007/s00253-018-9049-7. Epub 2018 May 23. PMID:29796971 doi:http://dx.doi.org/10.1007/s00253-018-9049-7

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/5xne"

Categories: Bacillus subtilis subsp. subtilis str. 168 | Large Structures | Feng Y | Ji F | Li M

@@ Line 3: / Line 3: @@
 <StructureSection load='5xne' size='340' side='right'caption='[[5xne]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5xne]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XNE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xne]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XNE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.501&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetolactate_decarboxylase Acetolactate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.5 4.1.1.5] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5xne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xne OCA], [http://pdbe.org/5xne PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xne RCSB], [http://www.ebi.ac.uk/pdbsum/5xne PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xne ProSAT]</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=5xne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xne OCA], [https://pdbe.org/5xne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xne RCSB], [https://www.ebi.ac.uk/pdbsum/5xne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xne ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ALDC_BACSU ALDC_BACSU]] Converts acetolactate into acetoin, which can be excreted by the cells. This may be a mechanism for controlling the internal pH of cells in the stationary stage.
+[https://www.uniprot.org/uniprot/ALDC_BACSU ALDC_BACSU] Converts acetolactate into acetoin, which can be excreted by the cells. This may be a mechanism for controlling the internal pH of cells in the stationary stage.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Acetolactate decarboxylase]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
 [[Category: Large Structures]]
-[[Category: Feng, Y]]
+[[Category: Feng Y]]
-[[Category: Ji, F]]
+[[Category: Ji F]]
-[[Category: Li, M]]
+[[Category: Li M]]
-[[Category: Lyase]]

5xne

From Proteopedia

Current revision

X-ray Crystal Structure of alpha-acetolactate decarboxylase from Bacillus subtilis strain 168

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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