1f1v: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(6 intermediate revisions by the same user not shown)
Line 1: Line 1:
==ANAEROBIC SUBSTRATE COMPLEX OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS. (COMPLEX WITH 3,4-DIHYDROXYPHENYLACETATE)==
==ANAEROBIC SUBSTRATE COMPLEX OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS. (COMPLEX WITH 3,4-DIHYDROXYPHENYLACETATE)==
<StructureSection load='1f1v' size='340' side='right' caption='[[1f1v]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='1f1v' size='340' side='right'caption='[[1f1v]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1f1v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F1V FirstGlance]. <br>
<table><tr><td colspan='2'>[[1f1v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F1V FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DHY:2-(3,4-DIHYDROXYPHENYL)ACETIC+ACID'>DHY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1f1r|1f1r]], [[1f1u|1f1u]], [[1f1x|1f1x]], [[1f1y|1f1y]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHY:2-(3,4-DIHYDROXYPHENYL)ACETIC+ACID'>DHY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3,4-dihydroxyphenylacetate_2,3-dioxygenase 3,4-dihydroxyphenylacetate 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.15 1.13.11.15] </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=1f1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1v OCA], [https://pdbe.org/1f1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f1v RCSB], [https://www.ebi.ac.uk/pdbsum/1f1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f1v ProSAT]</span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f1v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f1v RCSB], [http://www.ebi.ac.uk/pdbsum/1f1v PDBsum]</span></td></tr>
</table>
<table>
== Function ==
[https://www.uniprot.org/uniprot/Q44048_ARTGO Q44048_ARTGO]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f1/1f1v_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f1/1f1v_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1f1v ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+ and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four betaalphabetabetabeta modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.
Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases.,Vetting MW, Wackett LP, Que L Jr, Lipscomb JD, Ohlendorf DH J Bacteriol. 2004 Apr;186(7):1945-58. PMID:15028678<ref>PMID:15028678</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Dioxygenase|Dioxygenase]]
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]]
[[Category: Arthrobacter globiformis]]
[[Category: Arthrobacter globiformis]]
[[Category: Lipscomb, J D.]]
[[Category: Large Structures]]
[[Category: Ohlendorf, D H.]]
[[Category: Lipscomb JD]]
[[Category: Que, L.]]
[[Category: Ohlendorf DH]]
[[Category: Vetting, M W.]]
[[Category: Que Jr L]]
[[Category: Wackett, L P.]]
[[Category: Vetting MW]]
[[Category: Aromatic]]
[[Category: Wackett LP]]
[[Category: Biodegradation]]
[[Category: Dioxygenase]]
[[Category: Extradiol]]
[[Category: Manganese]]
[[Category: Oxidoreductase]]

Latest revision as of 10:09, 7 February 2024

ANAEROBIC SUBSTRATE COMPLEX OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS. (COMPLEX WITH 3,4-DIHYDROXYPHENYLACETATE)ANAEROBIC SUBSTRATE COMPLEX OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS. (COMPLEX WITH 3,4-DIHYDROXYPHENYLACETATE)

Structural highlights

1f1v is a 2 chain structure with sequence from Arthrobacter globiformis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q44048_ARTGO

Evolutionary Conservation

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

See Also

1f1v, resolution 1.90Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1f1v&oldid=4043100"