1iad: Difference between revisions

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== Structural highlights ==

<table><tr><td colspan='2'>[[1iad]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Astas Astas~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IAD FirstGlance]. <br>

<table><tr><td colspan='2'>[[1iad]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Astacus_astacus Astacus astacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IAD FirstGlance]. <br>

</td></tr><tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"~~><span class~~=~~'plainlinks'~~>[~~https://en.wikipedia.org/wiki/Astacin Astacin~~]~~, with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4~~.~~24.21~~ 3~~.4.24.21] </span>~~</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]] 2.3Å</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=1iad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iad OCA], [https://pdbe.org/1iad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iad RCSB], [https://www.ebi.ac.uk/pdbsum/1iad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iad ProSAT]</span></td></tr>

</table>

== Function ==

[[https://www.uniprot.org/uniprot/ASTA_ASTAS ASTA_ASTAS]] This protease prefers to cleave in front of small aliphatic residues (P1'). The presence of Lys or Arg in the P1 and P2 position yields high-turnover substrates. In the P3 position the enzyme prefers Pro > Val > Leu > Ala > Gly.

[https://www.uniprot.org/uniprot/ASTA_ASTAS ASTA_ASTAS] This protease prefers to cleave in front of small aliphatic residues (P1'). The presence of Lys or Arg in the P1 and P2 position yields high-turnover substrates. In the P3 position the enzyme prefers Pro > Val > Leu > Ala > Gly.

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Line 19:

</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1iad ConSurf].

~~<div style="background-color:#fffaf0;">~~

~~== Publication Abstract from PubMed ==~~

Astacin, a 200 residue digestive zinc-endopeptidase from the crayfish Astacus astacus L., is the prototype of the "astacin family", which comprises several membrane-bound mammalian endopeptidases and developmentally implicated regulatory proteins. Large trigonal crystals of astacin were grown, and X-ray reflection data to 1.8 A resolution were collected. The astacin structure has been solved by multiple isomorphous replacement using six heavy-atom derivatives, and refined to a crystallographic R-value of 0.158 applying stringent constraints. All 200 residues are clearly defined by electron density; 181 solvent molecules have been localized. Besides the native structure, the structures of Hg-astacin (with a mercury ion replacing the zinc) and of the apoenzyme were also refined. The astacin molecule exhibits a kidney-like shape. It consists of an amino-terminal and a carboxy-terminal domain, with a deep active-site cleft in between. The zinc ion, located at the bottom of this cleft, is co-ordinated in a novel trigonal-bipyramidal geometry by three histidine residues, a tyrosine and by a water molecule, which is also bound to the carboxylate side-chain of Glu93. The amino-terminal domain of astacin consists mainly of two long alpha-helices, one centrally located and one more peripheral, and of a five-stranded pleated beta-sheet. The amino terminus protrudes into an internal, water-filled cavity of the lower domain and forms a buried salt bridge with Glu103; amino-terminally extended pro-forms of astacin are thus not compatible with this structure. The carboxy-terminal domain of astacin is mainly organized in several turns and irregular structures. Because they share sequence identity of about 35%, the structures of the proteolytic domains of the other "astacin" members must be quite similar to astacin. Only a few very short deletions and insertions quite distant from the active-site distinguish their structures from astacin. The five-stranded beta-sheet and the two helices of the amino-terminal domain of astacin are topologically similar to the structure observed in the archetypal zinc-endopeptidase thermolysin; the rest of the structures are, in contrast, completely unrelated in astacin and thermolysin. The zinc ion, the central alpha-helix and the zinc-liganding residues His92, Glu93 and His96 of astacin are nearly superimposable with the respective groups of thermolysin, namely with the zinc ion, the "active-site helix", and His142TL, Glu143TL and His146TL of the zinc-binding consensus motif His-Glu-Xaa-Xaa-His (where Xaa is any amino acid residue).(ABSTRACT TRUNCATED AT 400 WORDS)

Refined 1.8 A X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L. Structure determination, refinement, molecular structure and comparison with thermolysin.,Gomis-Ruth FX, Stocker W, Huber R, Zwilling R, Bode W J Mol Biol. 1993 Feb 20;229(4):945-68. PMID:8445658<ref>PMID:8445658</ref>

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

~~</div>~~

~~<div class="pdbe-citations 1iad" style="background-color:#fffaf0;"></div>~~

==See Also==

*[[Proteinase|Proteinase]]

*[[Proteinase 3D structures|Proteinase 3D structures]]

~~== References ==~~

~~<references/>~~

__TOC__

</StructureSection>

[[Category: ~~Astacin]]~~

[[Category: Astacus astacus]]

~~[[Category: Astas~~]]

[[Category: Large Structures]]

[[Category: Bode, W]]

[[Category: Bode W]]

[[Category: Gomis-Rueth, F X]]

[[Category: Gomis-Rueth F-X]]

[[Category: Stoecker, W]]

[[Category: Stoecker W]]

~~[[Category: Zinc endopeptidase~~]]

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@@ Line 3: / Line 3: @@
 <StructureSection load='1iad' size='340' side='right'caption='[[1iad]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1iad]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Astas Astas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IAD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1iad]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Astacus_astacus Astacus astacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IAD FirstGlance]. <br>
-</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Astacin Astacin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.21 3.4.24.21] </span></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]] 2.3&#8491;</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=1iad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iad OCA], [https://pdbe.org/1iad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iad RCSB], [https://www.ebi.ac.uk/pdbsum/1iad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iad ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/ASTA_ASTAS ASTA_ASTAS]] This protease prefers to cleave in front of small aliphatic residues (P1'). The presence of Lys or Arg in the P1 and P2 position yields high-turnover substrates. In the P3 position the enzyme prefers Pro > Val > Leu > Ala > Gly.
+[https://www.uniprot.org/uniprot/ASTA_ASTAS ASTA_ASTAS] This protease prefers to cleave in front of small aliphatic residues (P1'). The presence of Lys or Arg in the P1 and P2 position yields high-turnover substrates. In the P3 position the enzyme prefers Pro > Val > Leu > Ala > Gly.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 19: / Line 19: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1iad ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Astacin, a 200 residue digestive zinc-endopeptidase from the crayfish Astacus astacus L., is the prototype of the "astacin family", which comprises several membrane-bound mammalian endopeptidases and developmentally implicated regulatory proteins. Large trigonal crystals of astacin were grown, and X-ray reflection data to 1.8 A resolution were collected. The astacin structure has been solved by multiple isomorphous replacement using six heavy-atom derivatives, and refined to a crystallographic R-value of 0.158 applying stringent constraints. All 200 residues are clearly defined by electron density; 181 solvent molecules have been localized. Besides the native structure, the structures of Hg-astacin (with a mercury ion replacing the zinc) and of the apoenzyme were also refined. The astacin molecule exhibits a kidney-like shape. It consists of an amino-terminal and a carboxy-terminal domain, with a deep active-site cleft in between. The zinc ion, located at the bottom of this cleft, is co-ordinated in a novel trigonal-bipyramidal geometry by three histidine residues, a tyrosine and by a water molecule, which is also bound to the carboxylate side-chain of Glu93. The amino-terminal domain of astacin consists mainly of two long alpha-helices, one centrally located and one more peripheral, and of a five-stranded pleated beta-sheet. The amino terminus protrudes into an internal, water-filled cavity of the lower domain and forms a buried salt bridge with Glu103; amino-terminally extended pro-forms of astacin are thus not compatible with this structure. The carboxy-terminal domain of astacin is mainly organized in several turns and irregular structures. Because they share sequence identity of about 35%, the structures of the proteolytic domains of the other "astacin" members must be quite similar to astacin. Only a few very short deletions and insertions quite distant from the active-site distinguish their structures from astacin. The five-stranded beta-sheet and the two helices of the amino-terminal domain of astacin are topologically similar to the structure observed in the archetypal zinc-endopeptidase thermolysin; the rest of the structures are, in contrast, completely unrelated in astacin and thermolysin. The zinc ion, the central alpha-helix and the zinc-liganding residues His92, Glu93 and His96 of astacin are nearly superimposable with the respective groups of thermolysin, namely with the zinc ion, the "active-site helix", and His142TL, Glu143TL and His146TL of the zinc-binding consensus motif His-Glu-Xaa-Xaa-His (where Xaa is any amino acid residue).(ABSTRACT TRUNCATED AT 400 WORDS)
-Refined 1.8 A X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L. Structure determination, refinement, molecular structure and comparison with thermolysin.,Gomis-Ruth FX, Stocker W, Huber R, Zwilling R, Bode W J Mol Biol. 1993 Feb 20;229(4):945-68. PMID:8445658<ref>PMID:8445658</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1iad" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Proteinase|Proteinase]]
+*[[Proteinase 3D structures|Proteinase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Astacin]]
+[[Category: Astacus astacus]]
-[[Category: Astas]]
 [[Category: Large Structures]]
-[[Category: Bode, W]]
+[[Category: Bode W]]
-[[Category: Gomis-Rueth, F X]]
+[[Category: Gomis-Rueth F-X]]
-[[Category: Stoecker, W]]
+[[Category: Stoecker W]]
-[[Category: Zinc endopeptidase]]