1g12

From Proteopedia

(Difference between revisions)

Current revision

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Structural highlights

1g12 is a 1 chain structure with sequence from Grifola frondosa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PLMP_GRIFR

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

Crystal structures of a peptidyl-Lys metalloendopeptidase (MEP) from the edible mushroom Grifola frondosa (GfMEP) were solved in four crystal forms. This represents the first structure of the new family 'aspzincins' with a novel active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs conserved among aspzincins. His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner. A Tyr133 side chain located on the S1' pocket had different configurations in two crystal forms and was not observed in the other crystal forms. The flexible Tyr133 plays two roles in the enzymatic function of GfMEP. The first is to provide a hydrophobic environment with Phe83 in order to accommodate the alkyl part of the Lys side chain of a substrate and the second is as a 'proton donor' to the oxyanion of the tetrahedral transition state to stabilize the reaction transition state.

Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms.,Hori T, Kumasaka T, Yamamoto M, Nonaka N, Tanaka N, Hashimoto Y, Ueki U, Takio K Acta Crystallogr D Biol Crystallogr. 2001 Mar;57(Pt 3):361-8. PMID:11223512^[1]

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

References

↑ Hori T, Kumasaka T, Yamamoto M, Nonaka N, Tanaka N, Hashimoto Y, Ueki U, Takio K. Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms. Acta Crystallogr D Biol Crystallogr. 2001 Mar;57(Pt 3):361-8. PMID:11223512

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/1g12"

@@ Line 3: / Line 3: @@
 <StructureSection load='1g12' size='340' side='right'caption='[[1g12]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1g12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Grifola_frondosa Grifola frondosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G12 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1g12]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Grifola_frondosa Grifola frondosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G12 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ge5|1ge5]], [[1ge6|1ge6]], [[1ge7|1ge7]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidyl-Lys_metalloendopeptidase Peptidyl-Lys metalloendopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.20 3.4.24.20] </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=1g12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g12 OCA], [https://pdbe.org/1g12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g12 RCSB], [https://www.ebi.ac.uk/pdbsum/1g12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g12 ProSAT]</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=1g12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g12 OCA], [http://pdbe.org/1g12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g12 RCSB], [http://www.ebi.ac.uk/pdbsum/1g12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1g12 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PLMP_GRIFR PLMP_GRIFR]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g1/1g12_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 34: / Line 35: @@
 [[Category: Grifola frondosa]]
 [[Category: Large Structures]]
-[[Category: Peptidyl-Lys metalloendopeptidase]]
+[[Category: Hashimoto Y]]
-[[Category: Hashimoto, Y]]
+[[Category: Hori T]]
-[[Category: Hori, T]]
+[[Category: Kumasaka T]]
-[[Category: Kumasaka, T]]
+[[Category: Nonaka T]]
-[[Category: Nonaka, T]]
+[[Category: Takio K]]
-[[Category: Takio, K]]
+[[Category: Tanaka N]]
-[[Category: Tanaka, N]]
+[[Category: Ueki T]]
-[[Category: Ueki, T]]
+[[Category: Yamamoto M]]
-[[Category: Yamamoto, M]]
-[[Category: Hydrolase]]
-[[Category: Metalloprotease]]
-[[Category: Zinc cordinate]]

1g12

From Proteopedia

Current revision

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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