2dqa

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Tapes japonica Lysozyme

Structural highlights

2dqa is a 2 chain structure with sequence from Ruditapes philippinarum. 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

LYS_RUDPH Bacteriolytic activity against Gram-positive bacterium M.luteus and thereby probably protects against bacterial infection (PubMed:14523554, PubMed:15249048, PubMed:9914527). Also has chitinase activity (PubMed:14523554, PubMed:15249048, PubMed:17631496, PubMed:9914527). May act as an ispopeptidase, cleaving isopeptide bonds between the side chains of Lys and Gln residues in proteins or in the cross-linking peptide of peptidoglycan in bacterial cell walls (PubMed:14523554, PubMed:15249048).^[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

Tapes japonica lysozyme (TJL) is classified as a member of the recently established i-type lysozyme family. In this study, we solved the crystal structure of TJL complexed with a trimer of N-acetylglucosamine to 1.6A resolution. Based on structure and mutation analyses, we demonstrated that Glu-18 and Asp-30 are the catalytic residues of TJL. Furthermore, the present findings suggest that the catalytic mechanism of TJL is a retaining mechanism that proceeds through a covalent sugar-enzyme intermediate. On the other hand, the quaternary structure in the crystal revealed a dimer formed by the electrostatic interactions of catalytic residues (Glu-18 and Asp-30) in one molecule with the positive residues at the C terminus in helix 6 of the other molecule. Gel chromatography analysis revealed that the TJL dimer remained intact under low salt conditions but that it dissociated to TJL monomers under high salt conditions. With increasing salt concentrations, the chitinase activity of TJL dramatically increased. Therefore, this study provides novel evidence that the lysozyme activity of TJL is modulated by its quaternary structure.

Crystal structure of Tapes japonica Lysozyme with substrate analogue: structural basis of the catalytic mechanism and manifestation of its chitinase activity accompanied by quaternary structural change.,Goto T, Abe Y, Kakuta Y, Takeshita K, Imoto T, Ueda T J Biol Chem. 2007 Sep 14;282(37):27459-67. Epub 2007 Jul 13. PMID:17631496^[5]

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

References

↑ Takeshita K, Hashimoto Y, Ueda T, Imoto T. A small chimerically bifunctional monomeric protein: Tapes japonica lysozyme. Cell Mol Life Sci. 2003 Sep;60(9):1944-51. PMID:14523554 doi:10.1007/s00018-003-3082-z
↑ Takeshita K, Hashimoto Y, Thujihata Y, So T, Ueda T, Iomoto T. Determination of the complete cDNA sequence, construction of expression systems, and elucidation of fibrinolytic activity for Tapes japonica lysozyme. Protein Expr Purif. 2004 Aug;36(2):254-62. PMID:15249048 doi:10.1016/j.pep.2004.05.001
↑ Goto T, Abe Y, Kakuta Y, Takeshita K, Imoto T, Ueda T. Crystal structure of Tapes japonica Lysozyme with substrate analogue: structural basis of the catalytic mechanism and manifestation of its chitinase activity accompanied by quaternary structural change. J Biol Chem. 2007 Sep 14;282(37):27459-67. Epub 2007 Jul 13. PMID:17631496 doi:10.1074/jbc.M704555200
↑ Ito Y, Yoshikawa A, Hotani T, Fukuda S, Sugimura K, Imoto T. Amino acid sequences of lysozymes newly purified from invertebrates imply wide distribution of a novel class in the lysozyme family. Eur J Biochem. 1999 Jan;259(1-2):456-61. PMID:9914527 doi:10.1046/j.1432-1327.1999.00064.x
↑ Goto T, Abe Y, Kakuta Y, Takeshita K, Imoto T, Ueda T. Crystal structure of Tapes japonica Lysozyme with substrate analogue: structural basis of the catalytic mechanism and manifestation of its chitinase activity accompanied by quaternary structural change. J Biol Chem. 2007 Sep 14;282(37):27459-67. Epub 2007 Jul 13. PMID:17631496 doi:10.1074/jbc.M704555200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2dqa"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Tapes japonica Lysozyme==
-<StructureSection load='2dqa' size='340' side='right' caption='[[2dqa]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='2dqa' size='340' side='right'caption='[[2dqa]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dqa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ruditapes_philippinarum Ruditapes philippinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dqa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruditapes_philippinarum Ruditapes philippinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQA FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>
+</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><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900017:triacetyl-beta-chitotriose'>PRD_900017</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dqa RCSB], [http://www.ebi.ac.uk/pdbsum/2dqa PDBsum]</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=2dqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqa OCA], [https://pdbe.org/2dqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dqa RCSB], [https://www.ebi.ac.uk/pdbsum/2dqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dqa ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LYS_RUDPH LYS_RUDPH] Bacteriolytic activity against Gram-positive bacterium M.luteus and thereby probably protects against bacterial infection (PubMed:14523554, PubMed:15249048, PubMed:9914527). Also has chitinase activity (PubMed:14523554, PubMed:15249048, PubMed:17631496, PubMed:9914527). May act as an ispopeptidase, cleaving isopeptide bonds between the side chains of Lys and Gln residues in proteins or in the cross-linking peptide of peptidoglycan in bacterial cell walls (PubMed:14523554, PubMed:15249048).<ref>PMID:14523554</ref> <ref>PMID:15249048</ref> <ref>PMID:17631496</ref> <ref>PMID:9914527</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/dq/2dqa_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dq/2dqa_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>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2dqa ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2dqa" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 32: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
 [[Category: Ruditapes philippinarum]]
-[[Category: Abe, Y.]]
+[[Category: Abe Y]]
-[[Category: Goto, T.]]
+[[Category: Goto T]]
-[[Category: Imoto, T.]]
+[[Category: Imoto T]]
-[[Category: Kakuta, Y.]]
+[[Category: Kakuta Y]]
-[[Category: Takeshita, K.]]
+[[Category: Takeshita K]]
-[[Category: Ueda, T.]]
+[[Category: Ueda T]]
-[[Category: Enzyme]]
-[[Category: Hydrolase]]
-[[Category: Lysozyme]]
-[[Category: Substrate complex]]

2dqa

From Proteopedia

Current revision

Crystal Structure of Tapes japonica Lysozyme

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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