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2b1n

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Current revision

Crystal structure of a papain-fold protein without the catalytic cysteine from seeds of Pachyrhizus erosus

Structural highlights

2b1n is a 2 chain structure with sequence from Pachyrhizus erosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q3Y6U7_9FABA

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 31kDa cysteine protease, SPE31, was isolated from the seeds of a legume plant, Pachyrizhus erosus. The protein was purified, crystallized and the 3D structure solved using molecular replacement. The cDNA was obtained by RT PCR followed by amplification using mRNA isolated from the seeds of the legume plant as a template. Analysis of the cDNA sequence and the 3D structure indicated the protein to belong to the papain family. Detailed analysis of the structure revealed an unusual replacement of the conserved catalytic Cys with Gly. Replacement of another conserved residue Ala/Gly by a Phe sterically blocks the access of the substrate to the active site. A polyethyleneglycol molecule and a natural peptide fragment were bound to the surface of the active site. Asn159 was found to be glycosylated. The SPE31 cDNA sequence shares several features with P34, a protein found in soybeans, that is implicated in plant defense mechanisms as an elicitor receptor binding to syringolide. P34 has also been shown to interact with vegetative storage proteins and NADH-dependent hydroxypyruvate reductase. These roles suggest that SPE31 and P34 form a unique subfamily within the papain family. The crystal structure of SPE31 complexed with a natural peptide ligand reveals a unique active site architecture. In addition, the clear evidence of glycosylated Asn159 provides useful information towards understanding the functional mechanism of SPE31/P34.

Crystal structure of a papain-fold protein without the catalytic residue: a novel member in the cysteine proteinase family.,Zhang M, Wei Z, Chang S, Teng M, Gong W J Mol Biol. 2006 Apr 21;358(1):97-105. Epub 2006 Feb 3. PMID:16497323^[1]

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

References

↑ Zhang M, Wei Z, Chang S, Teng M, Gong W. Crystal structure of a papain-fold protein without the catalytic residue: a novel member in the cysteine proteinase family. J Mol Biol. 2006 Apr 21;358(1):97-105. Epub 2006 Feb 3. PMID:16497323 doi:http://dx.doi.org/10.1016/j.jmb.2006.01.065

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/2b1n"

Categories: Large Structures | Pachyrhizus erosus | Chang S | Wei Z | Zhang M

@@ Line 1: / Line 1: @@
 ==Crystal structure of a papain-fold protein without the catalytic cysteine from seeds of Pachyrhizus erosus==
-<StructureSection load='2b1n' size='340' side='right' caption='[[2b1n]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='2b1n' size='340' side='right'caption='[[2b1n]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2b1n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pachyrhizus_erosus Pachyrhizus erosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B1N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2b1n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pachyrhizus_erosus Pachyrhizus erosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B1N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2b1m|2b1m]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=2b1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b1n OCA], [http://pdbe.org/2b1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b1n RCSB], [http://www.ebi.ac.uk/pdbsum/2b1n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2b1n 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=2b1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b1n OCA], [https://pdbe.org/2b1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b1n RCSB], [https://www.ebi.ac.uk/pdbsum/2b1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b1n ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q3Y6U7_9FABA Q3Y6U7_9FABA]
 == 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/b1/2b1n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b1/2b1n_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Pachyrhizus erosus]]
-[[Category: Chang, S]]
+[[Category: Chang S]]
-[[Category: Wei, Z]]
+[[Category: Wei Z]]
-[[Category: Zhang, M]]
+[[Category: Zhang M]]
-[[Category: Papain-like]]
-[[Category: Peptide fragment]]
-[[Category: Sugar binding protein]]

2b1n

From Proteopedia

Current revision

Crystal structure of a papain-fold protein without the catalytic cysteine from seeds of Pachyrhizus erosus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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