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4nzc

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Revision as of 08:47, 18 January 2023

Crystal structure of Chitinase D from Serratia proteamaculans at 1.45 Angstrom resolution

Structural highlights

4nzc is a 1 chain structure with sequence from Serratia proteamaculans 568. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A8GFD6_SERP5

Publication Abstract from PubMed

Chitinases are known to hydrolyze chitin polymers into smaller chitooligosaccharides. Chitinase from bacterium Serratia proteamaculans (SpChiD) is found to exhibit both hydrolysis and transglycosylation activities. SpChiD belongs to family 18 of glycosyl hydrolases (GH-18). The recombinant SpChiD was crystallized and its three-dimensional structure was determined at 1.49 A resolution. The structure was refined to an R-factor of 16.2%. SpChiD consists of 406 amino acid residues. The polypeptide chain of SpChiD adopts a (beta/alpha)8 triosephosphate isomerase (TIM) barrel structure. SpChiD contains three acidic residues, Asp149, Asp151 and Glu153 as part of its catalytic scheme. While both Asp149 and Glu153 adopt single conformations, Asp151 is observed in two conformations. The substrate binding cleft is partially obstructed by a protruding loop, Asn30 - Asp42 causing a considerable reduction in the number of available subsites in the substrate binding site. The positioning of loop, Asn30 - Asp42 appears to be responsible for the transglycosylation activity. The structure determination indicated the presence of sulfone Met89 (SMet89). The sulfone methionine residue is located on the surface of the protein at a site where extra domain is attached in other chitinases. This is the first structure of a single domain chitinase with hydrolytic and transglycosylation activities.

Structure of chitinase D from Serratia proteamaculans reveals the structural basis of its dual action of hydrolysis and transglycosylation.,Madhuprakash J, Singh A, Kumar S, Sinha M, Kaur P, Sharma S, Podile AR, Singh TP Int J Biochem Mol Biol. 2013 Dec 15;4(4):166-78. eCollection 2013. PMID:24380021^[1]

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

References

↑ Madhuprakash J, Singh A, Kumar S, Sinha M, Kaur P, Sharma S, Podile AR, Singh TP. Structure of chitinase D from Serratia proteamaculans reveals the structural basis of its dual action of hydrolysis and transglycosylation. Int J Biochem Mol Biol. 2013 Dec 15;4(4):166-78. eCollection 2013. PMID:24380021

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4nzc"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Chitinase D from Serratia proteamaculans at 1.45 Angstrom resolution==
-<StructureSection load='4nzc' size='340' side='right' caption='[[4nzc]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
+<StructureSection load='4nzc' size='340' side='right'caption='[[4nzc]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4nzc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Serp5 Serp5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NZC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NZC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4nzc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_proteamaculans_568 Serratia proteamaculans 568]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NZC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NZC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene></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=4nzc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nzc OCA], [https://pdbe.org/4nzc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nzc RCSB], [https://www.ebi.ac.uk/pdbsum/4nzc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nzc ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lgx|4lgx]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Spro_2725 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=399741 SERP5])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chitinase Chitinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.14 3.2.1.14] </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=4nzc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nzc OCA], [http://pdbe.org/4nzc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nzc RCSB], [http://www.ebi.ac.uk/pdbsum/4nzc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nzc ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A8GFD6_SERP5 A8GFD6_SERP5]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Chitinase]]
+[[Category: Large Structures]]
-[[Category: Serp5]]
+[[Category: Serratia proteamaculans 568]]
-[[Category: Kaur, P]]
+[[Category: Kaur P]]
-[[Category: Kumar, S]]
+[[Category: Kumar S]]
-[[Category: Madhuprakash, J]]
+[[Category: Madhuprakash J]]
-[[Category: Podile, A R]]
+[[Category: Podile AR]]
-[[Category: Sharma, S]]
+[[Category: Sharma S]]
-[[Category: Singh, A]]
+[[Category: Singh A]]
-[[Category: Singh, T P]]
+[[Category: Singh TP]]
-[[Category: Sinha, M]]
+[[Category: Sinha M]]
-[[Category: Chitinase d]]
-[[Category: Hydrolase]]
-[[Category: Tim barrel]]
-[[Category: Transglycosylation]]

4nzc

From Proteopedia

Revision as of 08:47, 18 January 2023

Crystal structure of Chitinase D from Serratia proteamaculans at 1.45 Angstrom resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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