This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1lgn

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 02:52, 10 September 2015

DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT

Structural highlights

1lgn is a 5 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Disease

[SAMP_HUMAN] Note=SAP is a precursor of amyloid component P which is found in basement membrane and associated with amyloid deposits.

Function

[SAMP_HUMAN] Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells. May also function as a calcium-dependent lectin.

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

Serum amyloid P component (SAP) is a glycoprotein that binds in a calcium-dependent fashion to a variety of ligands including other proteins, glycosaminoglycans and DNA. SAP is universally associated with the amyloid deposits in all forms of amyloidoses including Alzheimer's disease. Small-molecule ligands that displace SAP from amyloid fibrils and thereby expose the fibrils to proteolytic clearance mechanisms hold potential as drugs for the prevention and treatment of amyloidosis. We have carried out a screen for novel SAP ligands and have identified 2'-deoxyadenosine-5'-monophosphate (dAMP) as a ligand. The crystal structure of the SAP-dAMP complex determined at 2.8 A resolution (R = 0.232, R(free) = 0.252) reveals a decamer in which all interactions between SAP pentamers are mediated by the ligand. The stability of the decamer in solution has been demonstrated by gel filtration chromatography. The two calcium ions of SAP are bridged by the dAMP phosphate group and five hydrogen bonds are formed between the protein and the ligand, including specific interactions made by the adenine base. This mode of dAMP binding is not compatible with the nucleotide being part of double-helical DNA. The SAP-dAMP decamer is stabilized mainly by base-stacking of adjacent ligand molecules and possibly by electrostatic interactions involving the dAMP phosphate groups; decamerization buries 1000 A2 (2.6%) of the pentamer solvent-accessible surface. Ligand-induced decamerization of SAP, which utilizes the high cooperativity of a multiple-site interaction, may be a strategy to overcome the problems for drug design associated with the rather modest affinities of SAP for small-molecule ligands.

Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP.,Hohenester E, Hutchinson WL, Pepys MB, Wood SP J Mol Biol. 1997 Jun 20;269(4):570-8. PMID:9217261^[1]

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

References

↑ Hohenester E, Hutchinson WL, Pepys MB, Wood SP. Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP. J Mol Biol. 1997 Jun 20;269(4):570-8. PMID:9217261 doi:10.1006/jmbi.1997.1075

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1lgn"

@@ Line 4: / Line 4: @@
 <table><tr><td colspan='2'>[[1lgn]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LGN FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=1lgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lgn RCSB], [http://www.ebi.ac.uk/pdbsum/1lgn PDBsum]</span></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=1lgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgn OCA], [http://pdbe.org/1lgn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lgn RCSB], [http://www.ebi.ac.uk/pdbsum/1lgn PDBsum]</span></td></tr>
 </table>
 == Disease ==
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1lgn" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

1lgn

From Proteopedia

Revision as of 02:52, 10 September 2015

DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox