2pvp

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[[Image:2pvp.jpg|left|200px]]
 
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==Crystal structure of D-Alanine-D-Alanine Ligase from Helicobacter pylori==
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The line below this paragraph, containing "STRUCTURE_2pvp", creates the "Structure Box" on the page.
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<StructureSection load='2pvp' size='340' side='right'caption='[[2pvp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2pvp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_SS1 Helicobacter pylori SS1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PVP FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pvp OCA], [https://pdbe.org/2pvp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pvp RCSB], [https://www.ebi.ac.uk/pdbsum/2pvp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pvp ProSAT]</span></td></tr>
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{{STRUCTURE_2pvp| PDB=2pvp | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q2N4T5_HELPX Q2N4T5_HELPX] Cell wall formation.[HAMAP-Rule:MF_00047][SAAS:SAAS00232736]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pv/2pvp_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2pvp ConSurf].
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<div style="clear:both"></div>
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'''Crystal structure of D-Alanine-D-Alanine Ligase from Helicobacter pylori'''
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==See Also==
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*[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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D-Alanine-D-alanine ligase is the second enzyme in the D-Ala branch of bacterial cell wall peptidoglycan assembly, and recognized as an attractive antimicrobial target. In this work, the D-Ala-D-Ala ligase of Helicobacter pylori strain SS1 (HpDdl) was kinetically and structurally characterized. The determined apparent K(m) of ATP (0.87 muM), the K(m1) (1.89 mM) and K(m2) of D-Ala (627 mM), and the k(cat) (115 min(-1)) at pH 8.0 indicated its relatively weak binding affinity and poor catalytic activity against the substrate D-Ala in vitro. However, by complementary assay of expressing HpDdl in Escherichia coli Deltaddl mutant, HpDdl was confirmed to be capable of D-Ala-D-Ala ligating in vivo. Through sequence alignment with other members of the D-Ala-D-X ligase superfamily, HpDdl keeps two conservatively substituted residues (Ile16 and Leu241) and two nonconserved residues (Leu308 and Tyr311) broadly located in the active region of the enzyme. Kinetic analyses against the corresponding HpDdl mutants (I16V, L241Y, L241F, L308T, and Y311S) suggested that these residues, especially Leu308 and Tyr311, might partly contribute to the unique catalytic properties of the enzyme. This was fairly proved by the crystal structure of HpDdl, which revealed that there is a 3(10)-helix (including residues from Gly306 to Leu312) near the D-Ala binding region in the C-terminal domain, where HpDdl has two sequence deletions compared with other homologs. Such 3(10)-helix may participate in D-Ala binding and conformational change of the enzyme. Our present work hopefully provides useful information for understanding the D-Ala-D-Ala ligase of Helicobacter pylori. Proteins 2008. (c) 2008 Wiley-Liss, Inc.
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[[Category: Helicobacter pylori SS1]]
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[[Category: Large Structures]]
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==About this Structure==
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[[Category: Jiang H]]
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2PVP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PVP OCA].
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[[Category: Shen X]]
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[[Category: Wu D]]
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==Reference==
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[[Category: Zhang L]]
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Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori., Wu D, Zhang L, Kong Y, Du J, Chen S, Chen J, Ding J, Jiang H, Shen X, Proteins. 2008 Mar 4;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18320587 18320587]
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[[Category: D-alanine--D-alanine ligase]]
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[[Category: Helicobacter pylori]]
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[[Category: Single protein]]
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[[Category: Jiang, H.]]
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[[Category: Shen, X.]]
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[[Category: Wu, D.]]
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[[Category: Zhang, L.]]
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[[Category: D-alanine-d-alanine ligase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 13:52:25 2008''
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Current revision

Crystal structure of D-Alanine-D-Alanine Ligase from Helicobacter pylori

PDB ID 2pvp

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