4qdi: Difference between revisions

Line 1:

'''~~Unreleased~~ structure'''

==Crystal structure II of MurF from Acinetobacter baumannii==

== Structural highlights ==

<table><tr><td colspan='2'>[[4qdi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QDI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QDI FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qf5|4qf5]]</td></tr>

<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine_ligase UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.10 6.3.2.10] </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=4qdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qdi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qdi RCSB], [http://www.ebi.ac.uk/pdbsum/4qdi PDBsum]</span></td></tr>

</table>

== Function ==

[[http://www.uniprot.org/uniprot/B7GVN5_ACIB3 B7GVN5_ACIB3]] Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein.[RuleBase:RU004136]

== Publication Abstract from PubMed ==

MurF adds d-Ala-d-Ala dipeptide to UDP-N-acetylmuramyl-l-Ala-gamma-d-Glu-m-DAP (or l-Lys) in an ATP-dependent manner, which is the last step in the biosynthesis of monomeric precursor of peptidoglycan. Here we report crystal structures of two MurF-ATP complexes: the MurF-ATP complex and the MurF-ATP-UDP complex. The ATP-binding mode revealed by the crystal structure of the MurF-ATP complex confirms the previous biochemical demonstration that a carbamoylated lysine and two Mg(2+) ions are required for enzyme activity of MurF. The UDP-MurF interactions observed in the crystal structure of the MurF-ATP-UDP complex depict the characteristic substrate-binding mode of MurF. The emergence and dissemination of multidrug-resistant Acinetobacter baumannii strains are great threats to public health. Therefore, the structural information on A. baumannii MurF as a validated target for drug discovery will provide a framework to develop antibacterial agents against multidrug-resistant A. baumannii infections as well as to understand the reaction mechanism of MurF.

~~The entry 4qdi is ON HOLD until Paper Publication~~

ATP-binding mode including a carbamoylated lysine and two Mg(2+) ions, and substrate-binding mode in Acinetobacter baumannii MurF.,Cha SS, An YJ, Jeong CS, Yu JH, Chung KM Biochem Biophys Res Commun. 2014 Jul 25;450(2):1045-50. doi:, 10.1016/j.bbrc.2014.06.108. Epub 2014 Jun 27. PMID:24978312<ref>PMID:24978312</ref>

~~Authors: An~~, ~~Y.J., Jeong, C~~.S.~~, Cha, S.S~~.

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

</div>

~~Description~~: ~~Crystal structure II of MurF from Acinetobacter baumannii~~

== References ==

[[Category: ~~Unreleased Structures~~]]

[[Category: Cha, S.S]]

__TOC__

[[Category: Jeong, C.S]]

</StructureSection>

[[Category: ~~An, Y.J~~]]

[[Category: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase]]

[[Category: An, Y J]]

[[Category: Cha, S S]]

[[Category: Jeong, C S]]

[[Category: Ligase]]

[[Category: Udp-n-acetylmuramoyl-tripeptide-d-alanyl-d-ananine ligase]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+==Crystal structure II of MurF from Acinetobacter baumannii==
+<StructureSection load='4qdi' size='340' side='right' caption='[[4qdi]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4qdi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QDI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QDI FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qf5|4qf5]]</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine_ligase UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.10 6.3.2.10] </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=4qdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qdi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qdi RCSB], [http://www.ebi.ac.uk/pdbsum/4qdi PDBsum]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/B7GVN5_ACIB3 B7GVN5_ACIB3]] Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein.[RuleBase:RU004136]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+MurF adds d-Ala-d-Ala dipeptide to UDP-N-acetylmuramyl-l-Ala-gamma-d-Glu-m-DAP (or l-Lys) in an ATP-dependent manner, which is the last step in the biosynthesis of monomeric precursor of peptidoglycan. Here we report crystal structures of two MurF-ATP complexes: the MurF-ATP complex and the MurF-ATP-UDP complex. The ATP-binding mode revealed by the crystal structure of the MurF-ATP complex confirms the previous biochemical demonstration that a carbamoylated lysine and two Mg(2+) ions are required for enzyme activity of MurF. The UDP-MurF interactions observed in the crystal structure of the MurF-ATP-UDP complex depict the characteristic substrate-binding mode of MurF. The emergence and dissemination of multidrug-resistant Acinetobacter baumannii strains are great threats to public health. Therefore, the structural information on A. baumannii MurF as a validated target for drug discovery will provide a framework to develop antibacterial agents against multidrug-resistant A. baumannii infections as well as to understand the reaction mechanism of MurF.
-The entry 4qdi is ON HOLD  until Paper Publication
+ATP-binding mode including a carbamoylated lysine and two Mg(2+) ions, and substrate-binding mode in Acinetobacter baumannii MurF.,Cha SS, An YJ, Jeong CS, Yu JH, Chung KM Biochem Biophys Res Commun. 2014 Jul 25;450(2):1045-50. doi:, 10.1016/j.bbrc.2014.06.108. Epub 2014 Jun 27. PMID:24978312<ref>PMID:24978312</ref>
-Authors: An, Y.J., Jeong, C.S., Cha, S.S.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-Description: Crystal structure II of MurF from Acinetobacter baumannii
+== References ==
-[[Category: Unreleased Structures]]
+<references/>
-[[Category: Cha, S.S]]
+__TOC__
-[[Category: Jeong, C.S]]
+</StructureSection>
-[[Category: An, Y.J]]
+[[Category: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase]]
+[[Category: An, Y J]]
+[[Category: Cha, S S]]
+[[Category: Jeong, C S]]
+[[Category: Ligase]]
+[[Category: Udp-n-acetylmuramoyl-tripeptide-d-alanyl-d-ananine ligase]]