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3pep

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Revision as of 07:17, 29 November 2017

REVISED 2.3 ANGSTROMS STRUCTURE OF PORCINE PEPSIN. EVIDENCE FOR A FLEXIBLE SUBDOMAIN

Structural highlights

3pep is a 1 chain structure with sequence from Pig. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Activity:	Pepsin A, with EC number 3.4.23.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PEPA_PIG] Shows particularly broad specificity; although bonds involving phenylalanine and leucine are preferred, many others are also cleaved to some extent.

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

A revised three-dimensional crystal structure of ethanol-inhibited porcine pepsin refined to an R-factor of 0.171 at 2.3 A resolution is presented and compared to the refined structures of the fungal aspartic proteinases: penicillopepsin, rhizopuspepsin, and endothiapepsin. Pepsin is composed of two nearly equal N and C domains related by an intra dyad. The overall polypeptide fold and active site structures are homologous for pepsin and the fungal enzymes. The weak inhibition of pepsin by ethanol can be explained by the presence of one or more ethanol molecules, in the vicinity of the active site carboxylates, which slightly alter the hydrogen-bonding network and which may compete with substrate binding in the active site. Structural superposition analysis showed that the N domains aligned better than the C-domains for pepsin and the fungal aspartic proteinases: 107-140 C alpha pairs aligned to 0.72-0.85 A rms for the N domains; 64-95 C alpha pairs aligned to 0.78-1.03 A rms for the C domains. The major structural difference between pepsin and the fungal enzymes concerns a newly described subdomain whose conformation varies markedly among these enzyme structures. The subdomain in pepsin comprises nearly 100 residues and is composed of two contiguous segments within the C domain (residues 192-212 and 223-299). the subdomain is connected, or "hinged," to a mixed beta-sheet that forms one of the structurally invariant, active site psi-loops. Relative subdomain displacements as large as a 21.0 degrees rotation and a 5.9 A translation were observed among the different enzymes. There is some suggestion in pepsin that the subdomain may be flexible and perhaps plays a structural role in mediating substrate binding, determining the substrate specificity, or in the activation of the zymogen.

Revised 2.3 A structure of porcine pepsin: evidence for a flexible subdomain.,Abad-Zapatero C, Rydel TJ, Erickson J Proteins. 1990;8(1):62-81. PMID:2217165^[1]

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

References

↑ Abad-Zapatero C, Rydel TJ, Erickson J. Revised 2.3 A structure of porcine pepsin: evidence for a flexible subdomain. Proteins. 1990;8(1):62-81. PMID:2217165 doi:http://dx.doi.org/10.1002/prot.340080109

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3pep"

Categories: Pepsin A | Pig | Abad-Zapatero, C | Erickson, J W

@@ Line 1: / Line 1: @@
 ==REVISED 2.3 ANGSTROMS STRUCTURE OF PORCINE PEPSIN. EVIDENCE FOR A FLEXIBLE SUBDOMAIN==
 <StructureSection load='3pep' size='340' side='right' caption='[[3pep]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pepsin_A Pepsin A], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.1 3.4.23.1] </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=3pep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pep OCA], [http://pdbe.org/3pep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pep RCSB], [http://www.ebi.ac.uk/pdbsum/3pep 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=3pep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pep OCA], [http://pdbe.org/3pep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pep RCSB], [http://www.ebi.ac.uk/pdbsum/3pep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pep ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 3pep" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Pepsin|Pepsin]]
 == References ==
 <references/>

3pep

From Proteopedia

Revision as of 07:17, 29 November 2017

REVISED 2.3 ANGSTROMS STRUCTURE OF PORCINE PEPSIN. EVIDENCE FOR A FLEXIBLE SUBDOMAIN

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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