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1rwf

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Crystal structure of Arthrobacter aurescens chondroitin AC lyase in complex with chondroitin tetrasaccharide

Structural highlights

1rwf 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 1.45Å
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.

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^[1]

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

References

↑ Lunin VV, Li Y, Linhardt RJ, Miyazono H, Kyogashima M, Kaneko T, Bell AW, Cygler M. High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism. J Mol Biol. 2004 Mar 19;337(2):367-86. PMID:15003453 doi:10.1016/j.jmb.2003.12.071

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/1rwf"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Arthrobacter aurescens chondroitin AC lyase in complex with chondroitin tetrasaccharide==
-<StructureSection load='1rwf' size='340' side='right' caption='[[1rwf]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
+<StructureSection load='1rwf' size='340' side='right'caption='[[1rwf]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1rwf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_aurescens Arthrobacter aurescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RWF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1rwf]] 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=1RWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RWF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ASG:2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE'>ASG</scene>, <scene name='pdbligand=GAD:2,6-ANHYDRO-3-DEOXY-D-ERYTHRO-HEX-2-ENONIC+ACID'>GAD</scene>, <scene name='pdbligand=GCT:4,5-DIHYDROXY-TETRAHYDRO-PYRAN-2-CARBOXYLIC+ACID'>GCT</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]] 1.45&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1rw9|1rw9]], [[1rwa|1rwa]], [[1rwc|1rwc]], [[1rwg|1rwg]], [[1rwh|1rwh]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASG:2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE'>ASG</scene>, <scene name='pdbligand=GAD:2,6-ANHYDRO-3-DEOXY-D-ERYTHRO-HEX-2-ENONIC+ACID'>GAD</scene>, <scene name='pdbligand=GCT:4,5-DIHYDROXY-TETRAHYDRO-PYRAN-2-CARBOXYLIC+ACID'>GCT</scene>, <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'>[http://en.wikipedia.org/wiki/Chondroitin_AC_lyase Chondroitin AC lyase], with EC number [http://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=1rwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwf OCA], [https://pdbe.org/1rwf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rwf RCSB], [https://www.ebi.ac.uk/pdbsum/1rwf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rwf 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=1rwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwf OCA], [http://pdbe.org/1rwf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rwf RCSB], [http://www.ebi.ac.uk/pdbsum/1rwf PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/P84141_PAEAU P84141_PAEAU]
 == 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/rw/1rwf_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rw/1rwf_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Arthrobacter aurescens]]
+[[Category: Large Structures]]
-[[Category: Chondroitin AC lyase]]
+[[Category: Paenarthrobacter aurescens]]
-[[Category: Bell, A W]]
+[[Category: Bell AW]]
-[[Category: Cygler, M]]
+[[Category: Cygler M]]
-[[Category: Kyogashima, M]]
+[[Category: Kyogashima M]]
-[[Category: Li, Y]]
+[[Category: Li Y]]
-[[Category: Lunin, V V]]
+[[Category: Lunin VV]]
-[[Category: Miyazono, H]]
+[[Category: Miyazono H]]
-[[Category: Chondroitin]]
-[[Category: Chondroitin lyase]]
-[[Category: Chondroitinase]]
-[[Category: Lyase]]

1rwf

From Proteopedia

Current revision

Crystal structure of Arthrobacter aurescens chondroitin AC lyase in complex with chondroitin tetrasaccharide

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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