3b8i: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:3b8i.jpg|left|200px]]<br /><applet load="3b8i" size="350" color="white" frame="true" align="right" spinBox="true"
caption="3b8i, resolution 1.90&Aring;" />
'''Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.'''<br />


==Overview==
==Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.==
Pseudomonas aeruginosa PA4872 was identified by sequence analysis as a structurally and functionally novel member of the PEP mutase/isocitrate lyase superfamily and therefore targeted for investigation. Substrate screens ruled out overlap with known catalytic functions of superfamily members. The crystal structure of PA4872 in complex with oxalate (a stable analogue of the shared family alpha-oxyanion carboxylate intermediate/transition state) and Mg2+ was determined at 1.9 A resolution. As with other PEP mutase/isocitrate lyase superfamily members, the protein assembles into a dimer of dimers with each subunit adopting an alpha/beta barrel fold and two subunits swapping their barrel's C-terminal alpha-helices. Mg2+ and oxalate bind in the same manner as observed with other superfamily members. The active site gating loop, known to play a catalytic role in the PEP mutase and lyase branches of the superfamily, adopts an open conformation. The Nepsilon of His235, an invariant residue in the PA4872 sequence family, is oriented toward a C(2) oxygen of oxalate analogous to the C(3) of a pyruvyl moiety. Deuterium exchange into alpha-oxocarboxylate-containing compounds was confirmed by 1H NMR spectroscopy. Having ruled out known activities, the involvement of a pyruvate enolate intermediate suggested a decarboxylase activity of an alpha-oxocarboxylate substrate. Enzymatic assays led to the discovery that PA4872 decarboxylates oxaloacetate (kcat = 7500 s(-1) and Km = 2.2 mM) and 3-methyloxaloacetate (kcat = 250 s(-1) and Km = 0.63 mM). Genome context of the fourteen sequence family members indicates that the enzyme is used by select group of Gram-negative bacteria to maintain cellular concentrations of bicarbonate and pyruvate; however the decarboxylation activity cannot be attributed to a pathway common to the various bacterial species.
<StructureSection load='3b8i' size='340' side='right'caption='[[3b8i]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[3b8i]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B8I FirstGlance]. <br>
3B8I is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa] with <scene name='pdbligand=OXL:'>OXL</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Oxaloacetate_decarboxylase Oxaloacetate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.3 4.1.1.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8I OCA].
</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8i OCA], [https://pdbe.org/3b8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b8i RCSB], [https://www.ebi.ac.uk/pdbsum/3b8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b8i ProSAT]</span></td></tr>
Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily., Narayanan BC, Niu W, Han Y, Zou J, Mariano PS, Dunaway-Mariano D, Herzberg O, Biochemistry. 2008 Jan 8;47(1):167-82. Epub 2007 Dec 15. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18081320 18081320]
</table>
[[Category: Oxaloacetate decarboxylase]]
== Function ==
[[Category: Pseudomonas aeruginosa]]
[https://www.uniprot.org/uniprot/OADC_PSEAE OADC_PSEAE] Catalyzes the decarboxylation of oxaloacetate into pyruvate with high efficiency. Is also able to decarboxylate 3-methyloxaloacetate. Seems to play a role in maintaining cellular concentrations of bicarbonate and pyruvate.<ref>PMID:18081320</ref>
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Herzberg, O]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Narayanan, B C.]]
Check<jmol>
[[Category: GOL]]
  <jmolCheckbox>
[[Category: MG]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b8/3b8i_consurf.spt"</scriptWhenChecked>
[[Category: OXL]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: alpha/beta barrel]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: helix swapping]]
  </jmolCheckbox>
[[Category: lyase]]
</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=3b8i ConSurf].
 
<div style="clear:both"></div>
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:04:18 2008''
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas aeruginosa PAO1]]
[[Category: Herzberg O]]
[[Category: Narayanan BC]]

Latest revision as of 09:28, 21 February 2024

Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.

3b8i, resolution 1.90Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=3b8i&oldid=4063427"