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2pvp

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Revision as of 15:34, 17 June 2021

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

Structural highlights

2pvp is a 2 chain structure with sequence from Helicobacter pylori (strain ss1). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	ddl (Helicobacter pylori (strain SS1))
Activity:	D-alanine--D-alanine ligase, with EC number 6.3.2.4
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.

Publication Abstract from PubMed

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.

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:18320587^[1]

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

References

↑ Wu D, Zhang L, Kong Y, Du J, Chen S, Chen J, Ding J, Jiang H, Shen X. Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori. Proteins. 2008 Mar 4;. PMID:18320587 doi:10.1002/prot.22009

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2pvp"

@@ Line 1: / Line 1: @@
 ==Crystal structure of D-Alanine-D-Alanine Ligase from Helicobacter pylori==
-<StructureSection load='2pvp' size='340' side='right' caption='[[2pvp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='2pvp' size='340' side='right'caption='[[2pvp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori_(strain_ss1) Helicobacter pylori (strain 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PVP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pvp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_(strain_ss1) Helicobacter pylori (strain 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>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=102617 Helicobacter pylori (strain SS1)])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddl ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=102617 Helicobacter pylori (strain SS1)])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </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=2pvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pvp OCA], [http://pdbe.org/2pvp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pvp RCSB], [http://www.ebi.ac.uk/pdbsum/2pvp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pvp ProSAT]</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=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>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q2N4T5_HELPX Q2N4T5_HELPX]] Cell wall formation.[HAMAP-Rule:MF_00047][SAAS:SAAS00232736]
+[[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]]
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[D-alanine-D-alanine ligase|D-alanine-D-alanine ligase]]
+*[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 37: @@
 </StructureSection>
 [[Category: D-alanine--D-alanine ligase]]
+[[Category: Large Structures]]
 [[Category: Jiang, H]]
 [[Category: Shen, X]]

2pvp

From Proteopedia

Revision as of 15:34, 17 June 2021

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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