1rw9: Difference between revisions

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<StructureSection load='1rw9' size='340' side='right'caption='[[1rw9]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
<StructureSection load='1rw9' size='340' side='right'caption='[[1rw9]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1rw9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_aurescens Arthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RW9 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1rw9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenarthrobacter_aurescens Paenarthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RW9 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.35&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rwa|1rwa]], [[1rwc|1rwc]], [[1rwf|1rwf]], [[1rwg|1rwg]], [[1rwh|1rwh]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.5 4.2.2.5] </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=1rw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rw9 OCA], [https://pdbe.org/1rw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rw9 RCSB], [https://www.ebi.ac.uk/pdbsum/1rw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rw9 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=1rw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rw9 OCA], [https://pdbe.org/1rw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rw9 RCSB], [https://www.ebi.ac.uk/pdbsum/1rw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rw9 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/P84141_PAEAU P84141_PAEAU]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1rw9 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=1rw9 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Chondroitin lyases (EC 4.2.2.4 and EC 4.2.2.5) are glycosaminoglycan-degrading enzymes that act as eliminases. Chondroitin lyase AC from Arthrobacter aurescens (ArthroAC) is known to act on chondroitin 4-sulfate and chondroitin 6-sulfate but not on dermatan sulfate. Like other chondroitin AC lyases, it is capable of cleaving hyaluronan. We have determined the three-dimensional crystal structure of ArthroAC in its native form as well as in complex with its substrates (chondroitin 4-sulfate tetrasaccharide, CS(tetra) and hyaluronan tetrasaccharide) at resolution varying from 1.25 A to 1.9A. The primary sequence of ArthroAC has not been previously determined but it was possible to determine the amino acid sequence of this enzyme from the high-resolution electron density maps and to confirm it by mass spectrometry. The enzyme-substrate complexes were obtained by soaking the substrate into the crystals for varying lengths of time (30 seconds to ten hours) and flash-cooling the crystals. The electron density map for crystals soaked in the substrate for as short as 30 seconds showed the substrate clearly and indicated that the ring of central glucuronic acid assumes a distorted boat conformation. This structure strongly supports the lytic mechanism where Tyr242 acts as a general base that abstracts the proton from the C5 position of glucuronic acid while Asn183 and His233 neutralize the charge on the glucuronate acidic group. Comparison of this structure with that of chondroitinase AC from Flavobacterium heparinum (FlavoAC) provides an explanation for the exolytic and endolytic mode of action of ArthroAC and FlavoAC, respectively.
High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism.,Lunin VV, Li Y, Linhardt RJ, Miyazono H, Kyogashima M, Kaneko T, Bell AW, Cygler M J Mol Biol. 2004 Mar 19;337(2):367-86. PMID:15003453<ref>PMID:15003453</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1rw9" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arthrobacter aurescens]]
[[Category: Chondroitin AC lyase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bell, A W]]
[[Category: Paenarthrobacter aurescens]]
[[Category: Cygler, M]]
[[Category: Bell AW]]
[[Category: Kaneko, T]]
[[Category: Cygler M]]
[[Category: Kyogashima, M]]
[[Category: Kaneko T]]
[[Category: Li, Y]]
[[Category: Kyogashima M]]
[[Category: Linhardt, R J]]
[[Category: Li Y]]
[[Category: Lunin, V V]]
[[Category: Linhardt RJ]]
[[Category: Miyazono, H]]
[[Category: Lunin VV]]
[[Category: Chondroitin lyase]]
[[Category: Miyazono H]]
[[Category: Chondroitinase]]
[[Category: Lyase]]

Latest revision as of 11:26, 14 February 2024

Crystal structure of the Arthrobacter aurescens chondroitin AC lyaseCrystal structure of the Arthrobacter aurescens chondroitin AC lyase

Structural highlights

1rw9 is a 1 chain structure with sequence from Paenarthrobacter aurescens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.35Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

P84141_PAEAU

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1rw9, resolution 1.35Å

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OCA
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