This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1f1v

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:09, 7 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1f1v.gif|left|200px]]<br /><applet load="1f1v" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1f1v, resolution 1.9&Aring;" />
 
-
'''ANAEROBIC SUBSTRATE COMPLEX OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS. (COMPLEX WITH 3,4-DIHYDROXYPHENYLACETATE)'''<br />
 
-
==Overview==
+
==ANAEROBIC SUBSTRATE COMPLEX OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS. (COMPLEX WITH 3,4-DIHYDROXYPHENYLACETATE)==
-
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.
+
<StructureSection load='1f1v' size='340' side='right'caption='[[1f1v]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<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 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 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 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>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q44048_ARTGO Q44048_ARTGO]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<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>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</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/main_output.php?pdb_ID=1f1v ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1F1V is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis] with <scene name='pdbligand=MN:'>MN</scene> and <scene name='pdbligand=DHY:'>DHY</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F1V OCA].
+
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15028678 15028678]
+
-
[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]]
+
[[Category: Arthrobacter globiformis]]
[[Category: Arthrobacter globiformis]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Jr., L Que.]]
+
[[Category: Lipscomb JD]]
-
[[Category: Lipscomb, J D.]]
+
[[Category: Ohlendorf DH]]
-
[[Category: Ohlendorf, D H.]]
+
[[Category: Que Jr L]]
-
[[Category: Vetting, M W.]]
+
[[Category: Vetting MW]]
-
[[Category: Wackett, L P.]]
+
[[Category: Wackett LP]]
-
[[Category: DHY]]
+
-
[[Category: MN]]
+
-
[[Category: aromatic]]
+
-
[[Category: biodegradation]]
+
-
[[Category: dioxygenase]]
+
-
[[Category: extradiol]]
+
-
[[Category: manganese]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:33:57 2008''
+

Current revision

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

PDB ID 1f1v

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1f1v"
Personal tools