4i42

From Proteopedia

(Difference between revisions)

Revision as of 08:39, 9 November 2022

E.coli. 1,4-dihydroxy-2-naphthoyl coenzyme A synthase (ecMenB) in complex with 1-hydroxy-2-naphthoyl-CoA

Structural highlights

4i42 is a 12 chain structure with sequence from Escherichia coli K-12. 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

MENB_ECOLI Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).^[1] ^[2]

Publication Abstract from PubMed

1, 4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase is a typical crotonase fold enzyme with an implicated role of conformational changes in catalysis. We have identified these conformational changes by determining the structures of its Escherichia coli and Synechocystis sp. PCC6803 orthologues in complex with a product analog. The structural changes include the folding of an active-site loop into a beta-hairpin and significant reorientation of a helix at the carboxy terminus. Interestingly, a new interface is formed between the ordered loop and the reoriented helix, both of which also form additional interactions with the coenzyme A moiety of the ligand. Site-directed mutation of the amino acid residues involved in these ligand-induced interactions significantly diminishes the enzyme activity. These results suggest a catalytically essential induced-fit that is likely initiated by the enzyme-ligand interactions at the active site.

Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme a synthase from the crotonase fold superfamily.,Sun Y, Song H, Li J, Li Y, Jiang M, Zhou J, Guo Z PLoS One. 2013 Apr 26;8(4):e63095. doi: 10.1371/journal.pone.0063095. Print 2013. PMID:23658663^[3]

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

References

↑ Young IG. Biosynthesis of bacterial menaquinones. Menaquinone mutants of Escherichia coli. Biochemistry. 1975 Jan 28;14(2):399-406. PMID:1091286
↑ Jiang M, Chen M, Guo ZF, Guo Z. A bicarbonate cofactor modulates 1,4-dihydroxy-2-naphthoyl-coenzyme a synthase in menaquinone biosynthesis of Escherichia coli. J Biol Chem. 2010 Sep 24;285(39):30159-69. doi: 10.1074/jbc.M110.147702. Epub, 2010 Jul 19. PMID:20643650 doi:10.1074/jbc.M110.147702
↑ Sun Y, Song H, Li J, Li Y, Jiang M, Zhou J, Guo Z. Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme a synthase from the crotonase fold superfamily. PLoS One. 2013 Apr 26;8(4):e63095. doi: 10.1371/journal.pone.0063095. Print 2013. PMID:23658663 doi:10.1371/journal.pone.0063095

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/4i42"

@@ Line 1: / Line 1: @@
 ==E.coli. 1,4-dihydroxy-2-naphthoyl coenzyme A synthase (ecMenB) in complex with 1-hydroxy-2-naphthoyl-CoA==
-<StructureSection load='4i42' size='340' side='right' caption='[[4i42]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='4i42' size='340' side='right'caption='[[4i42]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4i42]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I42 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4i42]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I42 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1HA:1-HYDROXY-2-NAPHTHOYL-COA'>1HA</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1HA:1-HYDROXY-2-NAPHTHOYL-COA'>1HA</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4elx|4elx]]</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=4i42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i42 OCA], [https://pdbe.org/4i42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i42 RCSB], [https://www.ebi.ac.uk/pdbsum/4i42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i42 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b2262, JW2257, menB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-dihydroxy-2-naphthoyl-CoA_synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </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=4i42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i42 OCA], [http://pdbe.org/4i42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i42 RCSB], [http://www.ebi.ac.uk/pdbsum/4i42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i42 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MENB_ECOLI MENB_ECOLI]] Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).<ref>PMID:1091286</ref> <ref>PMID:20643650</ref>
+[https://www.uniprot.org/uniprot/MENB_ECOLI MENB_ECOLI] Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).<ref>PMID:1091286</ref> <ref>PMID:20643650</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: 1,4-dihydroxy-2-naphthoyl-CoA synthase]]
+[[Category: Escherichia coli K-12]]
-[[Category: Ecoli]]
+[[Category: Large Structures]]
-[[Category: Guo, Z]]
+[[Category: Guo Z]]
-[[Category: Jiang, M]]
+[[Category: Jiang M]]
-[[Category: Li, J]]
+[[Category: Li J]]
-[[Category: Li, Y]]
+[[Category: Li Y]]
-[[Category: Song, H]]
+[[Category: Song H]]
-[[Category: Sun, Y]]
+[[Category: Sun Y]]
-[[Category: Zhou, J]]
+[[Category: Zhou J]]
-[[Category: Lyase]]

4i42

From Proteopedia

Revision as of 08:39, 9 November 2022

E.coli. 1,4-dihydroxy-2-naphthoyl coenzyme A synthase (ecMenB) in complex with 1-hydroxy-2-naphthoyl-CoA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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