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4hpn

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Crystal structure of a proposed galactarolactone cycloisomerase from Agrobacterium Tumefaciens, target EFI-500704, with bound Ca, ordered loops

Structural highlights

4hpn is a 1 chain structure with sequence from Agrobacterium fabrum str. C58. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GCI_AGRFC Catalyzes the ring opening of D-galactaro-1,4-lactone to yield 5-keto-4-deoxy-D-glucarate (KDG) via a beta-elimination reaction. This is a step in the oxidative degradation pathway of D-galacturonate, which allows A.tumefaciens to utilize D-galacturonate as a sole carbon source. To a lesser extent, can also use D-glucaro-1,4-lactone as substrate to produce KDG, but cannot use D-galactaro-1,5-lactone, D-glucaro-6,3-lactone and linear D-glucarate.^[1] ^[2]

Publication Abstract from PubMed

Pectin is found in the cell wall of plants and is often discarded as waste. A number of research groups are interested in redirecting this biomass waste stream for the production of fuel and bulk chemicals. The primary monomeric subunit of this polysaccharide is D-galacturonate, a six-carbon acid sugar that is degraded in a five-step pathway to central metabolic intermediates by some bacteria, including Agrobacterium tumefaciens. In the third step of the pathway, D-galactaro-1,4-lactone is converted to 2-keto-3-deoxy-L-threo-hexarate by a member of the mandelate racemase subgroup of the enolase superfamily with a novel activity for the superfamily. The 1.6 A resolution structure of this enzyme was determined, revealing an overall modified (beta/alpha)7beta TIM-barrel domain, a hallmark of the superfamily. D-Galactaro-1,4-lactone was manually docked into the active site located at the interface between the N-terminal lid domain and the C-terminal barrel domain. On the basis of the position of the lactone in the active site, Lys166 is predicted to be the active-site base responsible for abstraction of the alpha proton. His296 on the opposite side of the active site is predicted to be the general acid that donates a proton to the beta carbon as the lactone ring opens. The lactone ring appears to be oriented within the active site by stacking interactions with Trp298.

Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation.,Vetting MW, Bouvier JT, Gerlt JA, Almo SC Acta Crystallogr F Struct Biol Commun. 2016 Jan;72(Pt 1):36-41. doi:, 10.1107/S2053230X15023286. Epub 2016 Jan 1. PMID:26750482^[3]

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

References

↑ Andberg M, Maaheimo H, Boer H, Penttila M, Koivula A, Richard P. Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate. J Biol Chem. 2012 May 18;287(21):17662-71. doi: 10.1074/jbc.M111.335240. Epub, 2012 Apr 5. PMID:22493433 doi:http://dx.doi.org/10.1074/jbc.M111.335240
↑ Bouvier JT, Groninger-Poe FP, Vetting M, Almo SC, Gerlt JA. Galactaro delta-lactone isomerase: lactone isomerization by a member of the amidohydrolase superfamily. Biochemistry. 2014 Feb 4;53(4):614-6. doi: 10.1021/bi5000492. Epub 2014 Jan 24. PMID:24450804 doi:http://dx.doi.org/10.1021/bi5000492
↑ Vetting MW, Bouvier JT, Gerlt JA, Almo SC. Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation. Acta Crystallogr F Struct Biol Commun. 2016 Jan;72(Pt 1):36-41. doi:, 10.1107/S2053230X15023286. Epub 2016 Jan 1. PMID:26750482 doi:http://dx.doi.org/10.1107/S2053230X15023286

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/4hpn"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a proposed galactarolactone cycloisomerase from Agrobacterium Tumefaciens, target EFI-500704, with bound Ca, ordered loops==
-<StructureSection load='4hpn' size='340' side='right' caption='[[4hpn]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='4hpn' size='340' side='right'caption='[[4hpn]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4hpn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrt5 Agrt5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HPN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4hpn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HPN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 1.6&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Atu3139 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRT5])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></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=4hpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hpn OCA], [http://pdbe.org/4hpn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hpn RCSB], [http://www.ebi.ac.uk/pdbsum/4hpn PDBsum]</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=4hpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hpn OCA], [https://pdbe.org/4hpn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hpn RCSB], [https://www.ebi.ac.uk/pdbsum/4hpn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hpn ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GCI_AGRT5 GCI_AGRT5]] Catalyzes the ring opening of D-galactaro-1,4-lactone to yield 5-keto-4-deoxy-D-glucarate (KDG) via a beta-elimination reaction. This is a step in the oxidative degradation pathway of D-galacturonate, which allows A.tumefaciens to utilize D-galacturonate as a sole carbon source. To a lesser extent, can also use D-glucaro-1,4-lactone as substrate to produce KDG, but cannot use D-galactaro-1,5-lactone, D-glucaro-6,3-lactone and linear D-glucarate.<ref>PMID:22493433</ref> <ref>PMID:24450804</ref>
+[https://www.uniprot.org/uniprot/GCI_AGRFC GCI_AGRFC] Catalyzes the ring opening of D-galactaro-1,4-lactone to yield 5-keto-4-deoxy-D-glucarate (KDG) via a beta-elimination reaction. This is a step in the oxidative degradation pathway of D-galacturonate, which allows A.tumefaciens to utilize D-galacturonate as a sole carbon source. To a lesser extent, can also use D-glucaro-1,4-lactone as substrate to produce KDG, but cannot use D-galactaro-1,5-lactone, D-glucaro-6,3-lactone and linear D-glucarate.<ref>PMID:22493433</ref> <ref>PMID:24450804</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Agrt5]]
+[[Category: Agrobacterium fabrum str. C58]]
-[[Category: Almo, S C]]
+[[Category: Large Structures]]
-[[Category: Bouvier, J T]]
+[[Category: Almo SC]]
-[[Category: EFI, Enzyme Function Initiative]]
+[[Category: Bouvier JT]]
-[[Category: Gerlt, J A]]
+[[Category: Gerlt JA]]
-[[Category: Imker, H J]]
+[[Category: Imker HJ]]
-[[Category: Morisco, L L]]
+[[Category: Morisco LL]]
-[[Category: Sojitra, S]]
+[[Category: Sojitra S]]
-[[Category: Vetting, M W]]
+[[Category: Vetting MW]]
-[[Category: Wasserman, S R]]
+[[Category: Wasserman SR]]
-[[Category: Efi]]
-[[Category: Enolase]]
-[[Category: Enzyme function initiative]]
-[[Category: Isomerase]]
-[[Category: Structural genomic]]

4hpn

From Proteopedia

Current revision

Crystal structure of a proposed galactarolactone cycloisomerase from Agrobacterium Tumefaciens, target EFI-500704, with bound Ca, ordered loops

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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