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3v8n

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Revision as of 06:42, 25 June 2020

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 8-bromo-5'-amino-5'-deoxyadenosine, reacted with a citrate molecule in N site

Structural highlights

3v8n is a 1 chain structure with sequence from "bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium monocytogenes hominis" nyfeldt 1932. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	2i2c, 3v7v, 3v7w, 3v7y, 3v80, 3v8m, 3v8p, 3v8q, 3v8r
Gene:	ppnK1, lmo0968 ("Bacterium monocytogenes hominis" Nyfeldt 1932)
Activity:	NAD(+) kinase, with EC number 2.7.1.23
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NADK1_LISMO] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]^[1] ^[2]

Publication Abstract from PubMed

Making new ligands for a given protein by in situ ligation of building blocks (or fragments) is an attractive method. However, it suffers from inherent limitations, such as the limited number of available chemical reactions and the low information content of usual chemical library deconvolution. Here, we describe a focused screening of adenosine derivatives using X-ray crystallography. We discovered an unexpected and biocompatible chemical reactivity and have simultaneously identified the mode of binding of the resulting products. We observed that the NAD kinase from Listeria monocytogenes (LmNADK1) can promote amide formation between 5'-amino-5'-deoxyadenosine and carboxylic acid groups. This unexpected reactivity allowed us to bridge in situ two adenosine derivatives to fully occupy the active NAD site. This guided the design of a close analog showing micromolar inhibition of two human pathogenic NAD kinases and potent bactericidal activity against Staphylococcus aureus in vitro.

Screening and In Situ Synthesis Using Crystals of a NAD Kinase Lead to a Potent Antistaphylococcal Compound.,Gelin M, Poncet-Montange G, Assairi L, Morellato L, Huteau V, Dugue L, Dussurget O, Pochet S, Labesse G Structure. 2012 May 16. PMID:22608967^[3]

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

References

↑ Poncet-Montange G, Assairi L, Arold S, Pochet S, Labesse G. NAD kinases use substrate-assisted catalysis for specific recognition of NAD. J Biol Chem. 2007 Nov 23;282(47):33925-34. Epub 2007 Aug 8. PMID:17686780 doi:10.1074/jbc.M701394200
↑ Gelin M, Poncet-Montange G, Assairi L, Morellato L, Huteau V, Dugue L, Dussurget O, Pochet S, Labesse G. Screening and In Situ Synthesis Using Crystals of a NAD Kinase Lead to a Potent Antistaphylococcal Compound. Structure. 2012 May 16. PMID:22608967 doi:10.1016/j.str.2012.03.024
↑ Gelin M, Poncet-Montange G, Assairi L, Morellato L, Huteau V, Dugue L, Dussurget O, Pochet S, Labesse G. Screening and In Situ Synthesis Using Crystals of a NAD Kinase Lead to a Potent Antistaphylococcal Compound. Structure. 2012 May 16. PMID:22608967 doi:10.1016/j.str.2012.03.024

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3v8n"

@@ Line 1: / Line 1: @@
 ==Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 8-bromo-5'-amino-5'-deoxyadenosine, reacted with a citrate molecule in N site==
-<StructureSection load='3v8n' size='340' side='right' caption='[[3v8n]], [[Resolution|resolution]] 2.38&Aring;' scene=''>
+<StructureSection load='3v8n' size='340' side='right'caption='[[3v8n]], [[Resolution|resolution]] 2.38&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3v8n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium monocytogenes hominis" nyfeldt 1932]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V8N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3v8n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_monocytogenes_hominis"_nyfeldt_1932 "bacterium monocytogenes hominis" nyfeldt 1932]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V8N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3V8N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CI:8-BROMO-5-{[3-CARBOXY-2-(CARBOXYMETHYL)-2-HYDROXYPROPANOYL]AMINO}-5-DEOXYADENOSINE'>5CI</scene>, <scene name='pdbligand=5NB:5-AMINO-8-BROMO-5-DEOXYADENOSINE'>5NB</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CI:8-BROMO-5-{[3-CARBOXY-2-(CARBOXYMETHYL)-2-HYDROXYPROPANOYL]AMINO}-5-DEOXYADENOSINE'>5CI</scene>, <scene name='pdbligand=5NB:5-AMINO-8-BROMO-5-DEOXYADENOSINE'>5NB</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2i2c|2i2c]], [[3v7v|3v7v]], [[3v7w|3v7w]], [[3v7y|3v7y]], [[3v80|3v80]], [[3v8m|3v8m]], [[3v8p|3v8p]], [[3v8q|3v8q]], [[3v8r|3v8r]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ppnK1, lmo0968 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1639 "Bacterium monocytogenes hominis" Nyfeldt 1932])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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=3v8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v8n OCA], [http://pdbe.org/3v8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3v8n RCSB], [http://www.ebi.ac.uk/pdbsum/3v8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3v8n ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3v8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v8n OCA], [http://pdbe.org/3v8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3v8n RCSB], [http://www.ebi.ac.uk/pdbsum/3v8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3v8n ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 26: / Line 26: @@
 </StructureSection>
 [[Category: Bacterium monocytogenes hominis nyfeldt 1932]]
+[[Category: Large Structures]]
 [[Category: Assairi, L]]
 [[Category: Dugu, L]]

3v8n

From Proteopedia

Revision as of 06:42, 25 June 2020

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 8-bromo-5'-amino-5'-deoxyadenosine, reacted with a citrate molecule in N site

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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