2pvp: Difference between revisions

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New page: left|200px {{Structure |PDB= 2pvp |SIZE=350|CAPTION= <scene name='initialview01'>2pvp</scene>, resolution 2.4Å |SITE= |LIGAND= |ACTIVITY= <span class='plainlin...
 
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[[Image:2pvp.jpg|left|200px]]


{{Structure
==Crystal structure of D-Alanine-D-Alanine Ligase from Helicobacter pylori==
|PDB= 2pvp |SIZE=350|CAPTION= <scene name='initialview01'>2pvp</scene>, resolution 2.4&Aring;
<StructureSection load='2pvp' size='340' side='right'caption='[[2pvp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<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>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </span>
</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>
|GENE= ddl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 Helicobacter pylori])
<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>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam07478 Dala_Dala_lig_C], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK01966 ddl], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01820 Dala_Dala_lig_N]</span>
</table>
|RELATEDENTRY=
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pvp OCA], [http://www.ebi.ac.uk/pdbsum/2pvp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pvp RCSB]</span>
[https://www.uniprot.org/uniprot/Q2N4T5_HELPX Q2N4T5_HELPX] Cell wall formation.[HAMAP-Rule:MF_00047][SAAS:SAAS00232736]
}}
== 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/pv/2pvp_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>


'''Crystal structure of D-Alanine-D-Alanine Ligase from Helicobacter pylori'''
==See Also==
 
*[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Helicobacter pylori SS1]]
 
[[Category: Large Structures]]
==About this Structure==
[[Category: Jiang H]]
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].
[[Category: Shen X]]
 
[[Category: Wu D]]
==Reference==
[[Category: Zhang L]]
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]
[[Category: D-alanine--D-alanine ligase]]
[[Category: Helicobacter pylori]]
[[Category: Single protein]]
[[Category: Jiang, H.]]
[[Category: Shen, X.]]
[[Category: Wu, D.]]
[[Category: Zhang, L.]]
[[Category: d-alanine-d-alanine ligase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 11:58:00 2008''

Latest revision as of 12:12, 21 February 2024

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

Structural highlights

2pvp is a 2 chain structure with sequence from Helicobacter pylori SS1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q2N4T5_HELPX Cell wall formation.[HAMAP-Rule:MF_00047][SAAS:SAAS00232736]

Evolutionary Conservation

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

See Also

2pvp, resolution 2.40Å

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