1b4u: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1b4u.gif|left|200px]]<br /><applet load="1b4u" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1b4u, resolution 2.2&Aring;" />
'''PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)'''<br />


==Overview==
==PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)==
BACKGROUND: Sphingomonas paucimobilis SYK-6 utilizes an extradiol-type catecholic dioxygenase, the LigAB enzyme (a protocatechuate 4,5-dioxygenase), to oxidize protocatechuate (or 3,4-dihydroxybenzoic acid, PCA). The enzyme belongs to the family of class III extradiol-type catecholic dioxygenases catalyzing the ring-opening reaction of protocatechuate and related compounds. The primary structure of LigAB suggests that the enzyme has no evolutionary relationship with the family of class II extradiol-type catecholic dioxygenases. Both the class II and class III enzymes utilize a non-heme ferrous center for adding dioxygen to the substrate. By elucidating the structure of LigAB, we aimed to provide a structural basis for discussing the function of class III enzymes. RESULTS: The crystal structure of substrate-free LigAB was solved at 2.2 A resolution. The molecule is an alpha2beta2 tetramer. The active site contains a non-heme iron coordinated by His12, His61, Glu242, and a water molecule located in a deep cleft of the beta subunit, which is covered by the alpha subunit. Because of the apparent oxidation of the Fe ion into the nonphysiological Fe(III) state, we could also solve the structure of LigAB complexed with a substrate, PCA. The iron coordination sphere in this complex is a distorted tetragonal bipyramid with one ligand missing, which is presumed to be the O2-binding site. CONCLUSIONS: The structure of LigAB is completely different from those of the class II extradiol-type dioxygenases exemplified by the BphC enzyme, a 2,3-dihydroxybiphenyl 1,2-dioxygenase from a Pseudomonas species. Thus, as already implicated by the primary structures, no evolutionary relationship exists between the class II and III enzymes. However, the two classes of enzymes share many geometrical characteristics with respect to the nature of the iron coordination sphere and the position of a putative catalytic base, strongly suggesting a common catalytic mechanism.
<StructureSection load='1b4u' size='340' side='right'caption='[[1b4u]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1b4u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B4U 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]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHB:3,4-DIHYDROXYBENZOIC+ACID'>DHB</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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=1b4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4u OCA], [https://pdbe.org/1b4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b4u RCSB], [https://www.ebi.ac.uk/pdbsum/1b4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b4u ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PCYA_SPHSK PCYA_SPHSK]
== 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/b4/1b4u_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=1b4u ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1B4U is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=DHB:'>DHB</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Protocatechuate_4,5-dioxygenase Protocatechuate 4,5-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.8 1.13.11.8] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4U OCA].
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions., Sugimoto K, Senda T, Aoshima H, Masai E, Fukuda M, Mitsui Y, Structure. 1999 Aug 15;7(8):953-65. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10467151 10467151]
[[Category: Large Structures]]
[[Category: Protein complex]]
[[Category: Protocatechuate 4,5-dioxygenase]]
[[Category: Sphingomonas paucimobilis]]
[[Category: Sphingomonas paucimobilis]]
[[Category: Mitsui, Y.]]
[[Category: Mitsui Y]]
[[Category: Senda, T.]]
[[Category: Senda T]]
[[Category: Sugimoto, K.]]
[[Category: Sugimoto K]]
[[Category: DHB]]
[[Category: FE]]
[[Category: extradiol type dioxygenase]]
[[Category: non-heme iron protein]]
[[Category: protocatechuate]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:51:29 2008''

Latest revision as of 09:34, 7 February 2024

PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)

Structural highlights

1b4u is a 4 chain structure with sequence from Sphingomonas paucimobilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PCYA_SPHSK

Evolutionary Conservation

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

See Also

1b4u, resolution 2.20Å

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=1b4u&oldid=4040452"