4ocp

From Proteopedia

(Difference between revisions)

Current revision

N-acetylhexosamine 1-phosphate kinase in complex with GlcNAc-1-phosphate and ADP

Structural highlights

4ocp is a 1 chain structure with sequence from Bifidobacterium longum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.938Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAHK_BIFL2 Phosphorylates both N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine (GalNAc) at similar rates. Involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria. Also accepts GTP and ITP as phosphate donors. In vitro, can phosphorylate several GlcNAc and GalNAc derivatives.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Utilization of N-acetylhexosamine in bifidobacteria requires the specific lacto-N-biose/galacto-N-biose pathway, a pathway differing from the Leloir pathway while establishing symbiosis between humans and bifidobacteria. The gene lnpB in the pathway encodes a novel hexosamine kinase NahK, which catalyzes the formation of N-acetylhexosamine 1-phosphate (GlcNAc-1P/GalNAc-1P). In this report, seven three-dimensional structures of NahK in complex with GlcNAc, GalNAc, GlcNAc-1P, GlcNAc/AMPPNP and GlcNAc-1P/ADP from both Bifidobacterium longum (JCM1217) and B. infantis (ATCC15697) were solved at resolutions of 1.5-2.2 A. NahK is a monomer in solution, and its polypeptide folds in a crescent-like architecture subdivided into two domains by a deep cleft. The NahK structures presented here represent the first multiple reaction complexes of the enzyme. This structural information reveals the molecular basis for the recognition of the given substrates and products, GlcNAc/GalNAc, GlcNAc-1P/GalNAc-1P, ATP/ADP and Mg(2+), and provides insights into the catalytic mechanism, enabling NahK and mutants thereof to form a choice of biocatalysts for enzymatic and chemoenzymatic synthesis of carbohydrates.

Insights into the binding specificity and catalytic mechanism of N-acetylhexosamine 1-phosphate kinases through multiple reaction complexes.,Wang KC, Lyu SY, Liu YC, Chang CY, Wu CJ, Li TL Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1401-10. doi:, 10.1107/S1399004714004209. Epub 2014 Apr 30. PMID:24816108^[4]

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

References

↑ Nishimoto M, Kitaoka M. Identification of N-acetylhexosamine 1-kinase in the complete lacto-N-biose I/galacto-N-biose metabolic pathway in Bifidobacterium longum. Appl Environ Microbiol. 2007 Oct;73(20):6444-9. Epub 2007 Aug 24. PMID:17720833 doi:http://dx.doi.org/10.1128/AEM.01425-07
↑ Cai L, Guan W, Kitaoka M, Shen J, Xia C, Chen W, Wang PG. A chemoenzymatic route to N-acetylglucosamine-1-phosphate analogues: substrate specificity investigations of N-acetylhexosamine 1-kinase. Chem Commun (Camb). 2009 May 28;(20):2944-6. doi: 10.1039/b904853g. Epub 2009 Apr, 24. PMID:19436918 doi:http://dx.doi.org/10.1039/b904853g
↑ Cai L, Guan W, Wang W, Zhao W, Kitaoka M, Shen J, O'Neil C, Wang PG. Substrate specificity of N-acetylhexosamine kinase towards N-acetylgalactosamine derivatives. Bioorg Med Chem Lett. 2009 Sep 15;19(18):5433-5. doi: 10.1016/j.bmcl.2009.07.104., Epub 2009 Jul 25. PMID:19683921 doi:http://dx.doi.org/10.1016/j.bmcl.2009.07.104
↑ Wang KC, Lyu SY, Liu YC, Chang CY, Wu CJ, Li TL. Insights into the binding specificity and catalytic mechanism of N-acetylhexosamine 1-phosphate kinases through multiple reaction complexes. Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1401-10. doi:, 10.1107/S1399004714004209. Epub 2014 Apr 30. PMID:24816108 doi:http://dx.doi.org/10.1107/S1399004714004209

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/4ocp"

@@ Line 1: / Line 1: @@
 ==N-acetylhexosamine 1-phosphate kinase in complex with GlcNAc-1-phosphate and ADP==
-<StructureSection load='4ocp' size='340' side='right' caption='[[4ocp]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
+<StructureSection load='4ocp' size='340' side='right'caption='[[4ocp]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ocp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OCP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OCP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ocp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OCP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GN1:2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>GN1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.938&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GN1:2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>GN1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ocj|4ocj]], [[4ock|4ock]], [[4oco|4oco]], [[4ocq|4ocq]], [[4ocu|4ocu]], [[4ocv|4ocv]]</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=4ocp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ocp OCA], [https://pdbe.org/4ocp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ocp RCSB], [https://www.ebi.ac.uk/pdbsum/4ocp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ocp ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylhexosamine_1-kinase N-acetylhexosamine 1-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.162 2.7.1.162] </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=4ocp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ocp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ocp RCSB], [http://www.ebi.ac.uk/pdbsum/4ocp PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/NAHK_BIFL2 NAHK_BIFL2] Phosphorylates both N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine (GalNAc) at similar rates. Involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria. Also accepts GTP and ITP as phosphate donors. In vitro, can phosphorylate several GlcNAc and GalNAc derivatives.<ref>PMID:17720833</ref> <ref>PMID:19436918</ref> <ref>PMID:19683921</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4ocp" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: N-acetylhexosamine 1-kinase]]
+[[Category: Bifidobacterium longum]]
-[[Category: Chang, C Y]]
+[[Category: Large Structures]]
-[[Category: Li, T L]]
+[[Category: Chang CY]]
-[[Category: Liu, Y C]]
+[[Category: Li TL]]
-[[Category: Lyu, S Y]]
+[[Category: Liu YC]]
-[[Category: Wang, K C]]
+[[Category: Lyu SY]]
-[[Category: Wu, C J]]
+[[Category: Wang KC]]
-[[Category: Kinase]]
+[[Category: Wu CJ]]
-[[Category: Transferase]]

4ocp

From Proteopedia

Current revision

N-acetylhexosamine 1-phosphate kinase in complex with GlcNAc-1-phosphate and ADP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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