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6gob

From Proteopedia

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Current revision

X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain

Structural highlights

6gob is a 1 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.96Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LYSC_CHICK Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.^[1]

Publication Abstract from PubMed

Pd(ii) and Pt(ii) compounds bearing N,N-pyridylbenzimidazole derivatives with an alkylated sulfonate or phosphonium side chain are able to bind the model protein lysozyme both covalently and non-covalently as an entire compound or as a product of a hydrolysis reaction. The interactions with the protein and the origin of the different behaviors of these complexes were unknown hitherto. Here, we present four crystal structures of their adducts with lysozyme. Pt- and Pd-containing fragments bind the protein with different stoichiometries close to the side chains of His15, Asp87, Asp101 and Asn77. The compounds bearing a phosphonium side chain degrade during the reaction with lysozyme. Data show the origin of the non-covalent mode of binding of Pd and Pt compounds bearing a sulfonate side chain, which drives the recognition process by forming a series of H-bonds and coulombic interactions with positively charged residue side chains. In a separate experiment, the structure of the adduct that is formed when the Pd(ii) compound containing an alkylated sulfonate group reacts with ribonuclease A was also determined. In this structure, the sulfonate-Pd(ii) complex binds the side chain of His105 on the surface of the protein and the side chain of the catalytically important His119 residue. Altogether, our data provide a structural basis for understanding the behavior of the analyzed Pd(ii)- and Pt(ii)-based cisplatin analogues in their reactions with proteins and show the first structural characterization of an adduct comprising a cisplatin analogue that is non-covalently bound to a protein. The results suggest that functionalization of a ligand system with a sulfonate group can significantly alter the protein-binding activity and thus the overall pharmacological profile of Pd(ii)- and Pt(ii)-based drugs.

Exploring the interactions between model proteins and Pd(ii) or Pt(ii) compounds bearing charged N,N-pyridylbenzimidazole bidentate ligands by X-ray crystallography.,Ferraro G, Mansour AM, Merlino A Dalton Trans. 2018 Jul 13. doi: 10.1039/c8dt01663a. PMID:30004541^[2]

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

References

↑ Maehashi K, Matano M, Irisawa T, Uchino M, Kashiwagi Y, Watanabe T. Molecular characterization of goose- and chicken-type lysozymes in emu (Dromaius novaehollandiae): evidence for extremely low lysozyme levels in emu egg white. Gene. 2012 Jan 15;492(1):244-9. doi: 10.1016/j.gene.2011.10.021. Epub 2011 Oct, 25. PMID:22044478 doi:10.1016/j.gene.2011.10.021
↑ Ferraro G, Mansour AM, Merlino A. Exploring the interactions between model proteins and Pd(ii) or Pt(ii) compounds bearing charged N,N-pyridylbenzimidazole bidentate ligands by X-ray crystallography. Dalton Trans. 2018 Jul 13. doi: 10.1039/c8dt01663a. PMID:30004541 doi:http://dx.doi.org/10.1039/c8dt01663a

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6gob"

Categories: Gallus gallus | Large Structures | Ferraro G | Merlino A

@@ Line 1: / Line 1: @@
 ==X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain==
-<StructureSection load='6gob' size='340' side='right' caption='[[6gob]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
+<StructureSection load='6gob' size='340' side='right'caption='[[6gob]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6gob]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GOB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GOB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6gob]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GOB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GOB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F6Q:N,N-pyridylbenzimidazole+derivative-Pd+complex'>F6Q</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PD:PALLADIUM+ION'>PD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F6Q:N,N-pyridylbenzimidazole+derivative-Pd+complex'>F6Q</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PD:PALLADIUM+ION'>PD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6gob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gob OCA], [http://pdbe.org/6gob PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gob RCSB], [http://www.ebi.ac.uk/pdbsum/6gob PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gob ProSAT]</span></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=6gob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gob OCA], [https://pdbe.org/6gob PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6gob RCSB], [https://www.ebi.ac.uk/pdbsum/6gob PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6gob ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
+[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 6gob" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 == References ==
 <references/>
@@ Line 24: / Line 27: @@
 </StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Ferraro, G]]
+[[Category: Ferraro G]]
-[[Category: Merlino, A]]
+[[Category: Merlino A]]
-[[Category: Hydrolase]]
-[[Category: N-pyridylbenzimidazole bidentate ligand]]
-[[Category: Non covalent bond]]
-[[Category: Palladium-based drug]]
-[[Category: Protein-metallodrug interaction]]
-[[Category: Stacking]]

6gob

From Proteopedia

Current revision

X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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