This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1xuz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:53, 14 February 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1xuz.jpg|left|200px]]
 
-
{{Structure
+
==Crystal structure analysis of sialic acid synthase (NeuB)from Neisseria meningitidis, bound to Mn2+, Phosphoenolpyruvate, and N-acetyl mannosaminitol==
-
|PDB= 1xuz |SIZE=350|CAPTION= <scene name='initialview01'>1xuz</scene>, resolution 2.2&Aring;
+
<StructureSection load='1xuz' size='340' side='right'caption='[[1xuz]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=MMN:5-DEOXY-5-{[(1S)-1-HYDROXYETHYL]AMINO}-D-GLUCITOL'>MMN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>
+
<table><tr><td colspan='2'>[[1xuz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis Neisseria meningitidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XUZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XUZ FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-
|GENE= neuB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=487 Neisseria meningitidis])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MMN:5-DEOXY-5-{[(1S)-1-HYDROXYETHYL]AMINO}-D-GLUCITOL'>MMN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xuz OCA], [https://pdbe.org/1xuz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xuz RCSB], [https://www.ebi.ac.uk/pdbsum/1xuz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xuz ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1xuu|1XUU]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xuz OCA], [http://www.ebi.ac.uk/pdbsum/1xuz PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xuz RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/Q57265_NEIME Q57265_NEIME]
-
 
+
== Evolutionary Conservation ==
-
'''Crystal structure analysis of sialic acid synthase (NeuB)from Neisseria meningitidis, bound to Mn2+, Phosphoenolpyruvate, and N-acetyl mannosaminitol'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xu/1xuz_consurf.spt"</scriptWhenChecked>
-
In Neisseria meningitidis and related bacterial pathogens, sialic acids play critical roles in mammalian cell immunity evasion and are synthesized by a conserved enzymatic pathway that includes sialic acid synthase (NeuB, SiaC, or SynC). NeuB catalyzes the condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine, directly forming N-acetylneuraminic acid (or sialic acid). In this paper we report the development of a coupled assay to monitor NeuB reaction kinetics and an 18O-labeling study that demonstrates the synthase operates via a C-O bond cleavage mechanism. We also report the first structure of a sialic acid synthase, that of NeuB, revealing a unique domain-swapped homodimer architecture consisting of a (beta/alpha)8 barrel (TIM barrel)-type fold at the N-terminal end and a domain with high sequence identity and structural similarity to the ice binding type III antifreeze proteins at the C-terminal end of the enzyme. We have determined the structures of NeuB in the malate-bound form and with bound PEP and the substrate analog N-acetylmannosaminitol to 1.9 and 2.2 A resolution, respectively. Typical of other TIM barrel proteins, the active site of NeuB is located in a cavity at the C-terminal end of the barrel; however, the positioning of the swapped antifreeze-like domain from the adjacent monomer provides key residues for hydrogen bonding with substrates in the active site of NeuB, a structural feature that leads to distinct modes of substrate binding from other PEP-utilizing enzymes that lack an analogous antifreeze-like domain. Our observation of a direct interaction between a highly ordered manganese and the N-acetylmannosaminitol in the NeuB active site also suggests an essential role for the ion as an electrophilic catalyst that activates the N-acetylmannosamine carbonyl to the addition of PEP.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1XUZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Neisseria_meningitidis Neisseria meningitidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XUZ OCA].
+
</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=1xuz ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
__TOC__
-
Structural and mechanistic analysis of sialic acid synthase NeuB from Neisseria meningitidis in complex with Mn2+, phosphoenolpyruvate, and N-acetylmannosaminitol., Gunawan J, Simard D, Gilbert M, Lovering AL, Wakarchuk WW, Tanner ME, Strynadka NC, J Biol Chem. 2005 Feb 4;280(5):3555-63. Epub 2004 Oct 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15516336 15516336]
+
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Neisseria meningitidis]]
[[Category: Neisseria meningitidis]]
-
[[Category: Single protein]]
+
[[Category: Gilbert M]]
-
[[Category: Gilbert, M.]]
+
[[Category: Gunawan J]]
-
[[Category: Gunawan, J.]]
+
[[Category: Lovering AL]]
-
[[Category: Lovering, A L.]]
+
[[Category: Simard D]]
-
[[Category: Simard, D.]]
+
[[Category: Strynadka NC]]
-
[[Category: Strynadka, N C.]]
+
[[Category: Tanner ME]]
-
[[Category: Tanner, M E.]]
+
[[Category: Wakarchuk WW]]
-
[[Category: Wakarchuk, W W.]]
+
-
[[Category: antifreeze-like domain]]
+
-
[[Category: domain-swapped dimer]]
+
-
[[Category: tim barrel]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:55:01 2008''
+

Current revision

Crystal structure analysis of sialic acid synthase (NeuB)from Neisseria meningitidis, bound to Mn2+, Phosphoenolpyruvate, and N-acetyl mannosaminitol

PDB ID 1xuz

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1xuz"
Personal tools