This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2zyc

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of peptidoglycan hydrolase from Sphingomonas sp. A1

Structural highlights

2zyc is a 1 chain structure with sequence from Sphingomonas sp. A1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.74Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B7XH69_9SPHN

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

Glycoside hydrolase (GH) categorized into family 73 plays an important role in degrading bacterial cell wall peptidoglycan. The flagellar protein FlgJ contains N- and C-terminal domains responsible for flagellar rod assembly and peptidoglycan hydrolysis, respectively. A member of family GH-73, the C-terminal domain (SPH1045-C) of FlgJ from Sphingomonas sp. strain A1 was expressed in Escherichia coli, purified, and characterized. SPH1045-C exhibited bacterial cell lytic activity most efficiently at pH 6.0 and 37 degrees C. The X-ray crystallographic structure of SPH1045-C was determined at 1.74 A resolution by single-wavelength anomalous diffraction. The enzyme consists of two lobes, alpha and beta. A deep cleft located between the two lobes can accommodate polymer molecules, suggesting that the active site is located in the cleft. Although SPH1045-C shows a structural homology with family GH-22 and GH-23 lysozymes, the arrangement of the nucleophile/base residue in the active site is specific to each peptidoglycan hydrolase.

Crystal structure of the glycosidase family 73 peptidoglycan hydrolase FlgJ.,Hashimoto W, Ochiai A, Momma K, Itoh T, Mikami B, Maruyama Y, Murata K Biochem Biophys Res Commun. 2009 Mar 27;381(1):16-21. Epub 2009 Feb 7. PMID:19351587^[1]

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

References

↑ Hashimoto W, Ochiai A, Momma K, Itoh T, Mikami B, Maruyama Y, Murata K. Crystal structure of the glycosidase family 73 peptidoglycan hydrolase FlgJ. Biochem Biophys Res Commun. 2009 Mar 27;381(1):16-21. Epub 2009 Feb 7. PMID:19351587 doi:10.1016/j.bbrc.2009.01.186

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/2zyc"

@@ Line 3: / Line 3: @@
 <StructureSection load='2zyc' size='340' side='right'caption='[[2zyc]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zyc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._a1 Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZYC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zyc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._A1 Sphingomonas sp. A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZYC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 1.74&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">flgJ ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90322 Sphingomonas sp. A1])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2zyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zyc OCA], [https://pdbe.org/2zyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zyc RCSB], [https://www.ebi.ac.uk/pdbsum/2zyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zyc ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/B7XH69_9SPHN B7XH69_9SPHN]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 34: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Sphingomonas sp. a1]]
+[[Category: Sphingomonas sp. A1]]
-[[Category: Hashimoto, W]]
+[[Category: Hashimoto W]]
-[[Category: Mikami, B]]
+[[Category: Mikami B]]
-[[Category: Murata, K]]
+[[Category: Murata K]]
-[[Category: Ochiai, A]]
+[[Category: Ochiai A]]
-[[Category: Hydrolase]]

2zyc

From Proteopedia

Current revision

Crystal structure of peptidoglycan hydrolase from Sphingomonas sp. A1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox