2a6l: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="2a6l" size="450" color="white" frame="true" align="right" spinBox="true" caption="2a6l, resolution 2.05Å" /> '''Dihydrodipicolinate ...
 
No edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2a6l.gif|left|200px]]<br /><applet load="2a6l" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2a6l, resolution 2.05&Aring;" />
'''Dihydrodipicolinate synthase (E. coli)- mutant R138H'''<br />


==Overview==
==Dihydrodipicolinate synthase (E. coli)- mutant R138H==
In plants and bacteria, the branch point of (S)-lysine biosynthesis is the, condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate, a, reaction catalyzed by dihydrodipicolinate synthase (DHDPS, EC 4.2.1.52)., It has been proposed that Arg138, a residue situated at the entrance to, the active site of DHDPS, is responsible for binding the carboxyl of, (S)-ASA and may additionally be involved in the mechanism of (S)-lysine, inhibition. This study tests these assertions by mutation of Arg138 to, both histidine and alanine. Following purification, DHDPS-R138H and, DHDPS-R138A each showed severely compromised activity (approximately 0.1%, that of the wild type), and the apparent Michaelis-Menten constant for, (S)-ASA in each mutant, calculated using a pseudo-single substrate, analysis, was significantly higher than that of the wild type. This, provides good evidence that Arg138 is indeed essential for catalysis and, plays a key role in substrate binding. To test whether structural changes, could account for the change in kinetic behavior, the solution structure, was probed via far-UV circular dichroism, confirming that the mutations at, position 138 did not modify secondary structure. The crystal structures of, both mutant enzymes were determined, confirming the presence of the, mutations and suggesting that Arg138 plays an important role in catalysis:, the stabilization of the catalytic triad residues, a motif we have, previously demonstrated to be essential for activity. In addition, the, role of Arg138 in (S)-lysine inhibition was examined. Both mutant enzymes, showed the same IC(50) values as the wild type but different partial, inhibition patterns, from which it is concluded that arginine 138 is not, essential for (S)-lysine inhibition.
<StructureSection load='2a6l' size='340' side='right'caption='[[2a6l]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2a6l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A6L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A6L 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]] 2.05&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [https://pdbe.org/2a6l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [https://www.ebi.ac.uk/pdbsum/2a6l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6l ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</ref>
== 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/a6/2a6l_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=2a6l ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2A6L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with K as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Dihydrodipicolinate_synthase Dihydrodipicolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.52 4.2.1.52] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2A6L OCA].
*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
 
== References ==
==Reference==
<references/>
Role of arginine 138 in the catalysis and regulation of Escherichia coli dihydrodipicolinate synthase., Dobson RC, Devenish SR, Turner LA, Clifford VR, Pearce FG, Jameson GB, Gerrard JA, Biochemistry. 2005 Oct 4;44(39):13007-13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16185069 16185069]
__TOC__
[[Category: Dihydrodipicolinate synthase]]
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Clifford, V.R.]]
[[Category: Clifford VR]]
[[Category: Devenish, S.R.]]
[[Category: Devenish SR]]
[[Category: Dobson, R.C.]]
[[Category: Dobson RC]]
[[Category: Gerrard, J.A.]]
[[Category: Gerrard JA]]
[[Category: Jameson, G.B.]]
[[Category: Jameson GB]]
[[Category: Pearce, F.G.]]
[[Category: Pearce FG]]
[[Category: Turner, L.A.]]
[[Category: Turner LA]]
[[Category: K]]
[[Category: beta-alpha-barrel]]
[[Category: dihydrodipicolinate synthase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:56:41 2007''

Latest revision as of 12:11, 14 February 2024

Dihydrodipicolinate synthase (E. coli)- mutant R138HDihydrodipicolinate synthase (E. coli)- mutant R138H

Structural highlights

2a6l is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.05Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DAPA_ECOLI Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).[1] [2]

Evolutionary Conservation

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

See Also

References

  1. ↑ Devenish SR, Blunt JW, Gerrard JA. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J Med Chem. 2010 Jun 24;53(12):4808-12. doi: 10.1021/jm100349s. PMID:20503968 doi:10.1021/jm100349s
  2. ↑ Blickling S, Renner C, Laber B, Pohlenz HD, Holak TA, Huber R. Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochemistry. 1997 Jan 7;36(1):24-33. PMID:8993314 doi:10.1021/bi962272d

2a6l, resolution 2.05Å

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=2a6l&oldid=4057627"