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6jqn

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Revision as of 02:14, 11 April 2020

Structure of PaaZ, a bifunctional enzyme in complex with NADP+ and OCoA

6jqn, resolution 3.10Å

Structural highlights

6jqn is a 6 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	paaZ (ECOLI)
Activity:	Oxepin-CoA hydrolase, with EC number 3.3.2.12
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PAAZ_ECOLI] Catalyzes the hydrolytic ring cleavage of 2-oxepin-2(3H)-ylideneacetyl-CoA (oxepin-CoA) via the open-chain aldehyde intermediate to yield 3-oxo-5,6-dehydrosuberyl-CoA. The enzyme consists of a C-terminal (R)-specific enoyl-CoA hydratase domain (formerly MaoC) that cleaves the ring and produces the highly reactive 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde and an N-terminal NADP-dependent aldehyde dehydrogenase domain that oxidizes the aldehyde to 3-oxo-5,6-dehydrosuberyl-CoA. Can also use crotonyl-CoA as substrate.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.

Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway.,Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR Nat Commun. 2019 Sep 11;10(1):4127. doi: 10.1038/s41467-019-11931-1. PMID:31511507^[4]

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

References

↑ Teufel R, Mascaraque V, Ismail W, Voss M, Perera J, Eisenreich W, Haehnel W, Fuchs G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14390-5. doi:, 10.1073/pnas.1005399107. Epub 2010 Jul 21. PMID:20660314 doi:10.1073/pnas.1005399107
↑ Teufel R, Gantert C, Voss M, Eisenreich W, Haehnel W, Fuchs G. Studies on the mechanism of ring hydrolysis in phenylacetate degradation: a metabolic branching point. J Biol Chem. 2011 Apr 1;286(13):11021-34. doi: 10.1074/jbc.M110.196667. Epub 2011, Feb 4. PMID:21296885 doi:http://dx.doi.org/10.1074/jbc.M110.196667
↑ Ferrandez A, Minambres B, Garcia B, Olivera ER, Luengo JM, Garcia JL, Diaz E. Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. J Biol Chem. 1998 Oct 2;273(40):25974-86. PMID:9748275
↑ Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR. Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway. Nat Commun. 2019 Sep 11;10(1):4127. doi: 10.1038/s41467-019-11931-1. PMID:31511507 doi:http://dx.doi.org/10.1038/s41467-019-11931-1

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/6jqn"

@@ Line 3: / Line 3: @@
 <SX load='6jqn' size='340' side='right' viewer='molstar' caption='[[6jqn]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6jqn]] is a 6 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=6JQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JQN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6jqn]] is a 6 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=6JQN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JQN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO8:OCTANOYL-COENZYME+A'>CO8</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO8:OCTANOYL-COENZYME+A'>CO8</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">paaZ ([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/Oxepin-CoA_hydrolase Oxepin-CoA hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.2.12 3.3.2.12] </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=6jqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqn OCA], [http://pdbe.org/6jqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jqn RCSB], [http://www.ebi.ac.uk/pdbsum/6jqn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqn ProSAT]</span></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=6jqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqn OCA], [http://pdbe.org/6jqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jqn RCSB], [http://www.ebi.ac.uk/pdbsum/6jqn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqn ProSAT]</span></td></tr>
 </table>
 == Function ==

6jqn

From Proteopedia

Revision as of 02:14, 11 April 2020

Structure of PaaZ, a bifunctional enzyme in complex with NADP+ and OCoA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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