2vun

From Proteopedia

(Difference between revisions)

Current revision

The Crystal Structure of Enamidase at 1.9 A Resolution - A new Member of the Amidohydrolase Superfamily

Structural highlights

2vun is a 4 chain structure with sequence from Eubacterium barkeri. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.89Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENA_EUBBA Decyclization of 6-oxo-1,4,5,6-tetrahydronicotinate to form 2-(enamine)glutarate, followed by hydrolysis to form (S)-2-formylglutarate.^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The hydrolysis of 1,4,5,6-tetrahydro-6-oxonicotinate to 2-formylglutarate is a central step in the catabolism of nicotinate in several Clostridia and Proteobacteria. This reaction is catalyzed by the novel enzyme enamidase, a new member of the amidohydrolase superfamily as indicated by its unique reaction, sequence relationship, and the stoichiometric binding of iron and zinc. A hallmark of enamidase is its capability to catalyze a two-step reaction: the initial decyclization of 1,4,5,6-tetrahydro-6-oxonicotinate leading to 2-(enamine)glutarate followed by an additional hydrolysis step yielding (S)-2-formylglutarate. Here, we present the crystal structure of enamidase from Eubacterium barkeri at 1.9 A resolution, providing a structural basis for catalysis and suggesting a mechanism for its exceptional activity and enantioselectivity. The enzyme forms a 222-symmetric tetramer built up by a dimer of dimers. Each enamidase monomer consists of a composite beta-sandwich domain and an (alpha/beta)(8)-TIM-barrel domain harboring the active site. With its catalytic binuclear metal center comprising both zinc and iron ions, enamidase represents a special case of subtype II amidohydrolases.

The crystal structure of enamidase: a bifunctional enzyme of the nicotinate catabolism.,Kress D, Alhapel A, Pierik AJ, Essen LO J Mol Biol. 2008 Dec 26;384(4):837-47. Epub 2008 Sep 12. PMID:18805424^[3]

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

References

↑ Alhapel A, Darley DJ, Wagener N, Eckel E, Elsner N, Pierik AJ. Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri. Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12341-6. Epub 2006 Aug 7. PMID:16894175 doi:http://dx.doi.org/10.1073/pnas.0601635103
↑ Kress D, Alhapel A, Pierik AJ, Essen LO. The crystal structure of enamidase: a bifunctional enzyme of the nicotinate catabolism. J Mol Biol. 2008 Dec 26;384(4):837-47. Epub 2008 Sep 12. PMID:18805424 doi:http://dx.doi.org/S0022-2836(08)01115-7
↑ Kress D, Alhapel A, Pierik AJ, Essen LO. The crystal structure of enamidase: a bifunctional enzyme of the nicotinate catabolism. J Mol Biol. 2008 Dec 26;384(4):837-47. Epub 2008 Sep 12. PMID:18805424 doi:http://dx.doi.org/S0022-2836(08)01115-7

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vun"

@@ Line 3: / Line 3: @@
 <StructureSection load='2vun' size='340' side='right'caption='[[2vun]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vun]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"inflabilis_barati"_(sic)_prevot_1938 "inflabilis barati" (sic) prevot 1938]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VUN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VUN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vun]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Eubacterium_barkeri Eubacterium barkeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VUN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VUN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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]] 1.89&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Enamidase Enamidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.18 3.5.2.18] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=2vun FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vun OCA], [https://pdbe.org/2vun PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vun RCSB], [https://www.ebi.ac.uk/pdbsum/2vun PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vun ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/ENA_EUBBA ENA_EUBBA]] Decyclization of 6-oxo-1,4,5,6-tetrahydronicotinate to form 2-(enamine)glutarate, followed by hydrolysis to form (S)-2-formylglutarate.<ref>PMID:16894175</ref> <ref>PMID:18805424</ref>
+[https://www.uniprot.org/uniprot/ENA_EUBBA ENA_EUBBA] Decyclization of 6-oxo-1,4,5,6-tetrahydronicotinate to form 2-(enamine)glutarate, followed by hydrolysis to form (S)-2-formylglutarate.<ref>PMID:16894175</ref> <ref>PMID:18805424</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Enamidase]]
+[[Category: Eubacterium barkeri]]
 [[Category: Large Structures]]
-[[Category: Alhapel, A]]
+[[Category: Alhapel A]]
-[[Category: Essen, L O]]
+[[Category: Essen L-O]]
-[[Category: Kress, D]]
+[[Category: Kress D]]
-[[Category: Pierik, A J]]
+[[Category: Pierik AJ]]
-[[Category: Amidohydrolase]]
-[[Category: Binuclear metal center]]
-[[Category: Hydrolase]]
-[[Category: Nicotinate degradation]]
-[[Category: Stereospecificity]]

2vun

From Proteopedia

Current revision

The Crystal Structure of Enamidase at 1.9 A Resolution - A new Member of the Amidohydrolase Superfamily

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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