3esd: Difference between revisions

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[[Image:3esd.png|left|200px]]


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==cut-2b; NCN-Pt-Pincer-Cutinase Hybrid==
The line below this paragraph, containing "STRUCTURE_3esd", creates the "Structure Box" on the page.
<StructureSection load='3esd' size='340' side='right'caption='[[3esd]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3esd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_vanettenii Fusarium vanettenii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ESD FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.22&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SXC:BROMO(4-{3-[(R)-ETHOXY(4-NITROPHENOXY)PHOSPHORYL]PROPYL}-2,6-BIS[(METHYLSULFANYL-KAPPAS)METHYL]PHENYL-KAPPAC~1~)PALLADIUM(2+)'>SXC</scene></td></tr>
{{STRUCTURE_3esd|  PDB=3esd  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3esd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esd OCA], [https://pdbe.org/3esd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3esd RCSB], [https://www.ebi.ac.uk/pdbsum/3esd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3esd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CUTI1_FUSVN CUTI1_FUSVN] Catalyzes the hydrolysis of complex carboxylic polyesters found in the cell wall of plants (PubMed:18658138, PubMed:19810726, PubMed:8286366, PubMed:8555209). Degrades cutin, a macromolecule that forms the structure of the plant cuticle (PubMed:18658138, PubMed:19810726, PubMed:8286366, PubMed:8555209). Allows pathogenic fungi to penetrate through the cuticular barrier into the host plant during the initial stage of fungal infection (Ref.4).<ref>PMID:18658138</ref> <ref>PMID:19810726</ref> <ref>PMID:8286366</ref> <ref>PMID:8555209</ref> [PROSITE-ProRule:PRU10109]
== 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/es/3esd_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3esd ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The first crystal structures of lipases that have been covalently modified through site-selective inhibition by different organometallic phosphonate-pincer-metal complexes are described. Two ECE-pincer-type d(8)-metal complexes, that is, platinum (1) or palladium (2) with phosphonate esters (ECE = [(EtO)-(O=)P(-O-C(6)H(4)-(NO(2))-4)(-C(3)H(6)-4-(C(6)H(2)-(CH(2)E)(2))](-) ; E = NMe(2) or SMe) were introduced prior to crystallization and have been shown to bind selectively to the Ser(120) residue in the active site of the lipase cutinase to give cut-1 (platinum) or cut-2 (palladium) hybrids. For all five presented crystal structures, the ECE-pincer-platinum or -palladium head group sticks out of the cutinase molecule and is exposed to the solvent. Depending on the nature of the ECE-pincer-metal head group, the ECE-pincer-platinum and -palladium guests occupy different pockets in the active site of cutinase, with concomitant different stereochemistries on the phosphorous atom for the cut-1 (S(P)) and cut-2 (R(P)) structures. When cut-1 was crystallized under halide-poor conditions, a novel metal-induced dimeric structure was formed between two cutinase-bound pincer-platinum head groups, which are interconnected through a single mu-Cl bridge. This halide-bridged metal dimer shows that coordination chemistry is possible with protein-modified pincer-metal complexes. Furthermore, we could use NCN-pincer-platinum complex 1 as site-selective tool for the phasing of raw protein diffraction data, which shows the potential use of pincer-platinum complex 1 as a heavy-atom derivative in protein crystallography.


===cut-2b; NCN-Pt-Pincer-Cutinase Hybrid===
Solid-state structural characterization of cutinase-ECE-pincer-metal hybrids.,Rutten L, Wieczorek B, Mannie JP, Kruithof CA, Dijkstra HP, Egmond MR, Lutz M, Klein Gebbink RJ, Gros P, van Koten G Chemistry. 2009;15(17):4270-80. PMID:19219875<ref>PMID:19219875</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3esd" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_19219875}}, adds the Publication Abstract to the page
*[[Cutinase 3D structures|Cutinase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 19219875 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_19219875}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Fusarium vanettenii]]
[[3esd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Nectria_haematococca_mpvi Nectria haematococca mpvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESD OCA].
[[Category: Large Structures]]
 
[[Category: Gros P]]
==Reference==
[[Category: Lutz M]]
<ref group="xtra">PMID:019219875</ref><references group="xtra"/>
[[Category: Mannie JPBA]]
[[Category: Cutinase]]
[[Category: Rutten L]]
[[Category: Nectria haematococca mpvi]]
[[Category: Gros, P.]]
[[Category: Lutz, M.]]
[[Category: Mannie, J P.B A.]]
[[Category: Rutten, L.]]
[[Category: Glycoprotein]]
[[Category: Hydrolase]]
[[Category: Protein-metallopincer complex]]
[[Category: Secreted]]
[[Category: Serine esterase]]

Latest revision as of 10:56, 9 October 2024

cut-2b; NCN-Pt-Pincer-Cutinase Hybridcut-2b; NCN-Pt-Pincer-Cutinase Hybrid

Structural highlights

3esd is a 1 chain structure with sequence from Fusarium vanettenii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.22Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CUTI1_FUSVN Catalyzes the hydrolysis of complex carboxylic polyesters found in the cell wall of plants (PubMed:18658138, PubMed:19810726, PubMed:8286366, PubMed:8555209). Degrades cutin, a macromolecule that forms the structure of the plant cuticle (PubMed:18658138, PubMed:19810726, PubMed:8286366, PubMed:8555209). Allows pathogenic fungi to penetrate through the cuticular barrier into the host plant during the initial stage of fungal infection (Ref.4).[1] [2] [3] [4] [PROSITE-ProRule:PRU10109]

Evolutionary Conservation

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

Publication Abstract from PubMed

The first crystal structures of lipases that have been covalently modified through site-selective inhibition by different organometallic phosphonate-pincer-metal complexes are described. Two ECE-pincer-type d(8)-metal complexes, that is, platinum (1) or palladium (2) with phosphonate esters (ECE = [(EtO)-(O=)P(-O-C(6)H(4)-(NO(2))-4)(-C(3)H(6)-4-(C(6)H(2)-(CH(2)E)(2))](-) ; E = NMe(2) or SMe) were introduced prior to crystallization and have been shown to bind selectively to the Ser(120) residue in the active site of the lipase cutinase to give cut-1 (platinum) or cut-2 (palladium) hybrids. For all five presented crystal structures, the ECE-pincer-platinum or -palladium head group sticks out of the cutinase molecule and is exposed to the solvent. Depending on the nature of the ECE-pincer-metal head group, the ECE-pincer-platinum and -palladium guests occupy different pockets in the active site of cutinase, with concomitant different stereochemistries on the phosphorous atom for the cut-1 (S(P)) and cut-2 (R(P)) structures. When cut-1 was crystallized under halide-poor conditions, a novel metal-induced dimeric structure was formed between two cutinase-bound pincer-platinum head groups, which are interconnected through a single mu-Cl bridge. This halide-bridged metal dimer shows that coordination chemistry is possible with protein-modified pincer-metal complexes. Furthermore, we could use NCN-pincer-platinum complex 1 as site-selective tool for the phasing of raw protein diffraction data, which shows the potential use of pincer-platinum complex 1 as a heavy-atom derivative in protein crystallography.

Solid-state structural characterization of cutinase-ECE-pincer-metal hybrids.,Rutten L, Wieczorek B, Mannie JP, Kruithof CA, Dijkstra HP, Egmond MR, Lutz M, Klein Gebbink RJ, Gros P, van Koten G Chemistry. 2009;15(17):4270-80. PMID:19219875[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Chen S, Tong X, Woodard RW, Du G, Wu J, Chen J. Identification and characterization of bacterial cutinase. J Biol Chem. 2008 Sep 19;283(38):25854-62. PMID:18658138 doi:10.1074/jbc.M800848200
  2. ↑ Liu Z, Gosser Y, Baker PJ, Ravee Y, Lu Z, Alemu G, Li H, Butterfoss GL, Kong XP, Gross R, Montclare JK. Structural and functional studies of Aspergillus oryzae cutinase: enhanced thermostability and hydrolytic activity of synthetic ester and polyester degradation. J Am Chem Soc. 2009 Nov 4;131(43):15711-6. PMID:19810726 doi:10.1021/ja9046697
  3. ↑ Martinez C, Nicolas A, van Tilbeurgh H, Egloff MP, Cudrey C, Verger R, Cambillau C. Cutinase, a lipolytic enzyme with a preformed oxyanion hole. Biochemistry. 1994 Jan 11;33(1):83-9. PMID:8286366
  4. ↑ Nicolas A, Egmond M, Verrips CT, de Vlieg J, Longhi S, Cambillau C, Martinez C. Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state. Biochemistry. 1996 Jan 16;35(2):398-410. PMID:8555209 doi:http://dx.doi.org/10.1021/bi9515578
  5. ↑ Rutten L, Wieczorek B, Mannie JP, Kruithof CA, Dijkstra HP, Egmond MR, Lutz M, Klein Gebbink RJ, Gros P, van Koten G. Solid-state structural characterization of cutinase-ECE-pincer-metal hybrids. Chemistry. 2009;15(17):4270-80. PMID:19219875 doi:10.1002/chem.200801995

3esd, resolution 1.22Å

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