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4fay

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Revision as of 04:45, 7 October 2022

Crystal structure of a trimeric bacterial microcompartment shell protein PduB with glycerol metabolites

Structural highlights

4fay is a 3 chain structure with sequence from Limosilactobacillus reuteri subsp. reuteri. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDUB_LIMRD One of the major shell proteins of the bacterial microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD) degradation (By similarity). Probably involved in a propanediol fermentation/reuterin formation pathway (Probable).[UniProtKB:P37449]^[1]

Publication Abstract from PubMed

Lactobacillus reuteri metabolizes two similar three-carbon molecules, 1,2-propanediol and glycerol, within closed polyhedral subcellular bacterial organelles called bacterial microcompartments (metabolosomes). The outer shell of the propanediol-utilization (Pdu) metabolosome is composed of hundreds of mainly hexagonal protein complexes made from six types of protein subunits that share similar domain structures. The structure of the bacterial microcompartment protein PduB has a tandem structural repeat within the subunit and assembles into a trimer with pseudo-hexagonal symmetry. This trimeric structure forms sheets in the crystal lattice and is able to fit within a polymeric sheet of the major shell component PduA to assemble a facet of the polyhedron. There are three pores within the trimer and these are formed between the tandem repeats within the subunits. The structure shows that each of these pores contains three glycerol molecules that interact with conserved residues, strongly suggesting that these subunit pores channel glycerol substrate into the metabolosome. In addition to the observation of glycerol occupying the subunit channels, the presence of glycerol on the molecular threefold symmetry axis suggests a role in locking closed the central region.

Substrate channels revealed in the trimeric Lactobacillus reuteri bacterial microcompartment shell protein PduB.,Pang A, Liang M, Prentice MB, Pickersgill RW Acta Crystallogr D Biol Crystallogr. 2012 Dec;68(Pt 12):1642-52. doi:, 10.1107/S0907444912039315. Epub 2012 Nov 9. PMID:23151629^[2]

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

References

↑ Frese SA, Benson AK, Tannock GW, Loach DM, Kim J, Zhang M, Oh PL, Heng NC, Patil PB, Juge N, Mackenzie DA, Pearson BM, Lapidus A, Dalin E, Tice H, Goltsman E, Land M, Hauser L, Ivanova N, Kyrpides NC, Walter J. The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet. 2011 Feb;7(2):e1001314. doi: 10.1371/journal.pgen.1001314. Epub 2011 , Feb 17. PMID:21379339 doi:http://dx.doi.org/10.1371/journal.pgen.1001314
↑ Pang A, Liang M, Prentice MB, Pickersgill RW. Substrate channels revealed in the trimeric Lactobacillus reuteri bacterial microcompartment shell protein PduB. Acta Crystallogr D Biol Crystallogr. 2012 Dec;68(Pt 12):1642-52. doi:, 10.1107/S0907444912039315. Epub 2012 Nov 9. PMID:23151629 doi:http://dx.doi.org/10.1107/S0907444912039315

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/4fay"

Categories: Large Structures | Limosilactobacillus reuteri subsp. reuteri | Pang AH | Pickersgill RW | Prentice MB

@@ Line 1: / Line 1: @@
 ==Crystal structure of a trimeric bacterial microcompartment shell protein PduB with glycerol metabolites==
-<StructureSection load='4fay' size='340' side='right' caption='[[4fay]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
+<StructureSection load='4fay' size='340' side='right'caption='[[4fay]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4fay]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lacrd Lacrd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FAY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4fay]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Limosilactobacillus_reuteri_subsp._reuteri Limosilactobacillus reuteri subsp. reuteri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FAY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Lreu_1748, PduB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=557436 LACRD])</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=4fay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fay OCA], [https://pdbe.org/4fay PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fay RCSB], [https://www.ebi.ac.uk/pdbsum/4fay PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fay 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=4fay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fay OCA], [http://pdbe.org/4fay PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fay RCSB], [http://www.ebi.ac.uk/pdbsum/4fay PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fay ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PDUB_LIMRD PDUB_LIMRD] One of the major shell proteins of the bacterial microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD) degradation (By similarity). Probably involved in a propanediol fermentation/reuterin formation pathway (Probable).[UniProtKB:P37449]<ref>PMID:21379339</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Lacrd]]
+[[Category: Large Structures]]
-[[Category: Pang, A H]]
+[[Category: Limosilactobacillus reuteri subsp. reuteri]]
-[[Category: Pickersgill, R W]]
+[[Category: Pang AH]]
-[[Category: Prentice, M B]]
+[[Category: Pickersgill RW]]
-[[Category: Bmc domain]]
+[[Category: Prentice MB]]
-[[Category: Glycerol-binding protein]]
-[[Category: Shell protein]]

4fay

From Proteopedia

Revision as of 04:45, 7 October 2022

Crystal structure of a trimeric bacterial microcompartment shell protein PduB with glycerol metabolites

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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