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| - | [[Image:1k7w.jpg|left|200px]] | |
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| - | {{Structure
| + | ==Crystal Structure of S283A Duck Delta 2 Crystallin Mutant== |
| - | |PDB= 1k7w |SIZE=350|CAPTION= <scene name='initialview01'>1k7w</scene>, resolution 1.96Å
| + | <StructureSection load='1k7w' size='340' side='right'caption='[[1k7w]], [[Resolution|resolution]] 1.96Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=AS1:ARGININOSUCCINATE'>AS1</scene>
| + | <table><tr><td colspan='2'>[[1k7w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Anas_platyrhynchos Anas platyrhynchos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K7W FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Argininosuccinate_lyase Argininosuccinate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.1 4.3.2.1] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AS1:ARGININOSUCCINATE'>AS1</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k7w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7w OCA], [https://pdbe.org/1k7w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k7w RCSB], [https://www.ebi.ac.uk/pdbsum/1k7w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k7w ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1hy1|1HY1]], [[1auw|1AUW]], [[1dcn|1DCN]], [[1hy0|1HY0]], [[1i0a|1I0A]], [[1aos|1AOS]], [[1k62|1K62]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k7w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7w OCA], [http://www.ebi.ac.uk/pdbsum/1k7w PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1k7w RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/ARLY2_ANAPL ARLY2_ANAPL] Delta crystallin, the principal crystallin in embryonic lens, is found only in birds and reptiles. This protein also functions as an enzymatically active argininosuccinate lyase.<ref>PMID:10029536</ref> <ref>PMID:11698398</ref> <ref>PMID:15320872</ref> <ref>PMID:9369472</ref> |
| | + | == 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/k7/1k7w_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </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=1k7w ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | The major soluble avian eye lens protein, delta crystallin, is highly homologous to the housekeeping enzyme argininosuccinate lyase (ASL). ASL is part of the urea and arginine-citrulline cycles and catalyzes the reversible breakdown of argininosuccinate to arginine and fumarate. In duck lenses, there are two delta crystallin isoforms that are 94% identical in amino acid sequence. Only the delta2 isoform has maintained ASL activity and has been used to investigate the enzymatic mechanism of ASL. The role of the active site residues Ser-29, Asp-33, Asp-89, Asn-116, Thr-161, His-162, Arg-238, Thr-281, Ser-283, Asn-291, Asp-293, Glu-296, Lys-325, Asp-330, and Lys-331 have been investigated by site-directed mutagenesis, and the structure of the inactive duck delta2 crystallin (ddeltac2) mutant S283A with bound argininosuccinate was determined at 1.96 A resolution. The S283A mutation does not interfere with substrate binding, because the 280's loop (residues 270-290) is in the open conformation and Ala-283 is more than 7 A from the substrate. The substrate is bound in a different conformation to that observed previously indicating a large degree of conformational flexibility in the fumarate moiety when the 280's loop is in the open conformation. The structure of the S283A ddeltac2 mutant and mutagenesis results reveal that a complex network of interactions of both protein residues and water molecules are involved in substrate binding and specificity. Small changes even to residues not involved directly in anchoring the argininosuccinate have a significant effect on catalysis. The results suggest that either His-162 or Thr-161 are responsible for proton abstraction and reinforce the putative role of Ser-283 as the catalytic acid, although we cannot eliminate the possibility that arginine is released in an uncharged form, with the solvent providing the required proton. A detailed enzymatic mechanism of ASL/ddeltac2 is presented. |
| | | | |
| - | '''Crystal Structure of S283A Duck Delta 2 Crystallin Mutant'''
| + | Mutational analysis of duck delta 2 crystallin and the structure of an inactive mutant with bound substrate provide insight into the enzymatic mechanism of argininosuccinate lyase.,Sampaleanu LM, Yu B, Howell PL J Biol Chem. 2002 Feb 8;277(6):4166-75. Epub 2001 Nov 6. PMID:11698398<ref>PMID:11698398</ref> |
| | | | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 1k7w" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Overview== | + | ==See Also== |
| - | The major soluble avian eye lens protein, delta crystallin, is highly homologous to the housekeeping enzyme argininosuccinate lyase (ASL). ASL is part of the urea and arginine-citrulline cycles and catalyzes the reversible breakdown of argininosuccinate to arginine and fumarate. In duck lenses, there are two delta crystallin isoforms that are 94% identical in amino acid sequence. Only the delta2 isoform has maintained ASL activity and has been used to investigate the enzymatic mechanism of ASL. The role of the active site residues Ser-29, Asp-33, Asp-89, Asn-116, Thr-161, His-162, Arg-238, Thr-281, Ser-283, Asn-291, Asp-293, Glu-296, Lys-325, Asp-330, and Lys-331 have been investigated by site-directed mutagenesis, and the structure of the inactive duck delta2 crystallin (ddeltac2) mutant S283A with bound argininosuccinate was determined at 1.96 A resolution. The S283A mutation does not interfere with substrate binding, because the 280's loop (residues 270-290) is in the open conformation and Ala-283 is more than 7 A from the substrate. The substrate is bound in a different conformation to that observed previously indicating a large degree of conformational flexibility in the fumarate moiety when the 280's loop is in the open conformation. The structure of the S283A ddeltac2 mutant and mutagenesis results reveal that a complex network of interactions of both protein residues and water molecules are involved in substrate binding and specificity. Small changes even to residues not involved directly in anchoring the argininosuccinate have a significant effect on catalysis. The results suggest that either His-162 or Thr-161 are responsible for proton abstraction and reinforce the putative role of Ser-283 as the catalytic acid, although we cannot eliminate the possibility that arginine is released in an uncharged form, with the solvent providing the required proton. A detailed enzymatic mechanism of ASL/ddeltac2 is presented.
| + | *[[Crystallin 3D structures|Crystallin 3D structures]] |
| - | | + | == References == |
| - | ==About this Structure==
| + | <references/> |
| - | 1K7W is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Anas_platyrhynchos Anas platyrhynchos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7W OCA].
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==Reference== | + | |
| - | Mutational analysis of duck delta 2 crystallin and the structure of an inactive mutant with bound substrate provide insight into the enzymatic mechanism of argininosuccinate lyase., Sampaleanu LM, Yu B, Howell PL, J Biol Chem. 2002 Feb 8;277(6):4166-75. Epub 2001 Nov 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11698398 11698398]
| + | |
| | [[Category: Anas platyrhynchos]] | | [[Category: Anas platyrhynchos]] |
| - | [[Category: Argininosuccinate lyase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Howell PL]] |
| - | [[Category: Howell, P L.]] | + | [[Category: Sampaleanu LM]] |
| - | [[Category: Sampaleanu, L M.]] | + | [[Category: Yu B]] |
| - | [[Category: Yu, B.]] | + | |
| - | [[Category: argininosuccinate lyase]]
| + | |
| - | [[Category: delta 2 crystallin]]
| + | |
| - | [[Category: enzyme mechanism]]
| + | |
| - | [[Category: eye lens protein]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:44:40 2008''
| + | |
| Structural highlights
Function
ARLY2_ANAPL Delta crystallin, the principal crystallin in embryonic lens, is found only in birds and reptiles. This protein also functions as an enzymatically active argininosuccinate lyase.[1] [2] [3] [4]
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
The major soluble avian eye lens protein, delta crystallin, is highly homologous to the housekeeping enzyme argininosuccinate lyase (ASL). ASL is part of the urea and arginine-citrulline cycles and catalyzes the reversible breakdown of argininosuccinate to arginine and fumarate. In duck lenses, there are two delta crystallin isoforms that are 94% identical in amino acid sequence. Only the delta2 isoform has maintained ASL activity and has been used to investigate the enzymatic mechanism of ASL. The role of the active site residues Ser-29, Asp-33, Asp-89, Asn-116, Thr-161, His-162, Arg-238, Thr-281, Ser-283, Asn-291, Asp-293, Glu-296, Lys-325, Asp-330, and Lys-331 have been investigated by site-directed mutagenesis, and the structure of the inactive duck delta2 crystallin (ddeltac2) mutant S283A with bound argininosuccinate was determined at 1.96 A resolution. The S283A mutation does not interfere with substrate binding, because the 280's loop (residues 270-290) is in the open conformation and Ala-283 is more than 7 A from the substrate. The substrate is bound in a different conformation to that observed previously indicating a large degree of conformational flexibility in the fumarate moiety when the 280's loop is in the open conformation. The structure of the S283A ddeltac2 mutant and mutagenesis results reveal that a complex network of interactions of both protein residues and water molecules are involved in substrate binding and specificity. Small changes even to residues not involved directly in anchoring the argininosuccinate have a significant effect on catalysis. The results suggest that either His-162 or Thr-161 are responsible for proton abstraction and reinforce the putative role of Ser-283 as the catalytic acid, although we cannot eliminate the possibility that arginine is released in an uncharged form, with the solvent providing the required proton. A detailed enzymatic mechanism of ASL/ddeltac2 is presented.
Mutational analysis of duck delta 2 crystallin and the structure of an inactive mutant with bound substrate provide insight into the enzymatic mechanism of argininosuccinate lyase.,Sampaleanu LM, Yu B, Howell PL J Biol Chem. 2002 Feb 8;277(6):4166-75. Epub 2001 Nov 6. PMID:11698398[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Vallee F, Turner MA, Lindley PL, Howell PL. Crystal structure of an inactive duck delta II crystallin mutant with bound argininosuccinate. Biochemistry. 1999 Feb 23;38(8):2425-34. PMID:10029536 doi:10.1021/bi982149h
- ↑ Sampaleanu LM, Yu B, Howell PL. Mutational analysis of duck delta 2 crystallin and the structure of an inactive mutant with bound substrate provide insight into the enzymatic mechanism of argininosuccinate lyase. J Biol Chem. 2002 Feb 8;277(6):4166-75. Epub 2001 Nov 6. PMID:11698398 doi:10.1074/jbc.M107465200
- ↑ Sampaleanu LM, Codding PW, Lobsanov YD, Tsai M, Smith GD, Horvatin C, Howell PL. Structural studies of duck delta2 crystallin mutants provide insight into the role of Thr161 and the 280s loop in catalysis. Biochem J. 2004 Dec 1;384(Pt 2):437-47. PMID:15320872 doi:10.1042/BJ20040656
- ↑ Abu-Abed M, Turner MA, Vallee F, Simpson A, Slingsby C, Howell PL. Structural comparison of the enzymatically active and inactive forms of delta crystallin and the role of histidine 91. Biochemistry. 1997 Nov 18;36(46):14012-22. PMID:9369472 doi:10.1021/bi971407s
- ↑ Sampaleanu LM, Yu B, Howell PL. Mutational analysis of duck delta 2 crystallin and the structure of an inactive mutant with bound substrate provide insight into the enzymatic mechanism of argininosuccinate lyase. J Biol Chem. 2002 Feb 8;277(6):4166-75. Epub 2001 Nov 6. PMID:11698398 doi:10.1074/jbc.M107465200
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