1cl2: 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:1cl2.gif|left|200px]]<br /><applet load="1cl2" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1cl2, resolution 2.2&Aring;" />
'''CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI IN COMPLEX WITH AMINOETHOXYVINYLGLYCINE'''<br />


==Overview==
==CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI IN COMPLEX WITH AMINOETHOXYVINYLGLYCINE==
The pyridoxal 5'-phosphate (PLP)-dependent cystathionine beta-lyase (CBL) was previously found to be inhibited by the natural toxins rhizobitoxine and l-aminoethoxyvinylglycine (AVG). The present study characterizes the interaction of Escherichia coli CBL with AVG and methoxyvinylglycine (MVG) by a combination of kinetic methods and X-ray crystallography. Upon AVG treatment, time-dependent, slow-binding inhibition [Morrison, J. F. (1982) Trends Biochem. Sci. 7, 102-105] was observed due to the generation of a long-lived, slowly dissociating enzyme-inhibitor complex. Kinetic analysis revealed a one-step inhibition mechanism (CBL + AVG --&gt; CBLAVG, Ki = 1.1 +/- 0.3 microM) with an association rate constant (k1) of 336 +/- 40 M-1 s-1. This value is several orders of magnitude lower than typical bimolecular rate constants of ES formation, suggesting that additional steps occur before formation of the first detectable CBLAVG complex. Loss of activity is paralleled by the conversion of the pyridoxaldimine 426 nm chromophore to a 341 nm-absorbing species. On the basis of the recently solved structure of native CBL [Clausen, T., et al. (1996) J. Mol. Biol. 262, 202-224], it was possible to elucidate the X-ray structure of the CBLAVG complex and to refine it to an R-factor of 16.4% at 2.2 A resolution. The refined structure reveals the geometry of the bound inhibitor and its interactions with residues in the active site of CBL. Both the X-ray structure and the absorbance spectrum of the CBLAVG complex are compatible with a ketimine as the reaction product. Thus, the inhibitor seems to bind in a similar way to CBL as the substrate, but after alpha-proton abstraction, the reaction proceeds in a CBL nontypical manner, i.e. protonation of PLP-C4', resulting in the "dead-end" ketimine PLP derivative. The CBLAVG structure furthermore suggests a binding mode for rhizobitoxine and explains the failure of MVG to inhibit CBL.
<StructureSection load='1cl2' size='340' side='right'caption='[[1cl2]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1cl2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CL2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CL2 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=PPG:(2E,3E)-4-(2-AMINOETHOXY)-2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)IMINO]BUT-3-ENOIC+ACID'>PPG</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=1cl2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cl2 OCA], [https://pdbe.org/1cl2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cl2 RCSB], [https://www.ebi.ac.uk/pdbsum/1cl2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cl2 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/METC_ECOLI METC_ECOLI]
== 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/cl/1cl2_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=1cl2 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1CL2 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 <scene name='pdbligand=PPG:'>PPG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Cystathionine_beta-lyase Cystathionine beta-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.8 4.4.1.8] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CL2 OCA].
*[[Cystathionine beta-lyase|Cystathionine beta-lyase]]
 
__TOC__
==Reference==
</StructureSection>
Slow-binding inhibition of Escherichia coli cystathionine beta-lyase by L-aminoethoxyvinylglycine: a kinetic and X-ray study., Clausen T, Huber R, Messerschmidt A, Pohlenz HD, Laber B, Biochemistry. 1997 Oct 14;36(41):12633-43. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9376370 9376370]
[[Category: Escherichia coli K-12]]
[[Category: Cystathionine beta-lyase]]
[[Category: Large Structures]]
[[Category: Escherichia coli]]
[[Category: Clausen T]]
[[Category: Single protein]]
[[Category: Huber R]]
[[Category: Clausen, T.]]
[[Category: Messerschmidt A]]
[[Category: Huber, R.]]
[[Category: Messerschmidt, A.]]
[[Category: PPG]]
[[Category: aminoethoxyvinylglycine]]
[[Category: c-s beta lyase]]
[[Category: methionine biosynthesis]]
[[Category: plp-dependent enzymes]]
[[Category: slow-binding inhibition]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:07:09 2008''

Latest revision as of 09:43, 7 February 2024

CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI IN COMPLEX WITH AMINOETHOXYVINYLGLYCINECYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI IN COMPLEX WITH AMINOETHOXYVINYLGLYCINE

Structural highlights

1cl2 is a 2 chain structure with sequence from Escherichia coli K-12. 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

METC_ECOLI

Evolutionary Conservation

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

See Also

1cl2, 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=1cl2&oldid=4041167"