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[[Image:1gqc.gif|left|200px]]<br />
<applet load="1gqc" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1gqc, resolution 2.6&Aring;" />
'''THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE COMPLEXED WITH CMP-KDO AT 100K'''<br />


==Overview==
==THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE COMPLEXED WITH CMP-Kdo at 100K==
The activation of the sugar 2-keto-3-deoxy-manno-octonic acid (Kdo) is, catalyzed by CMP-Kdo synthetase (EC 2.7.7.38) and results in a, monophosphate diester with CMP. The enzyme is a pharmaceutical target, because CMP-Kdo is required for the biosynthesis of lipopolysaccharides, that are vital for Gram-negative bacteria. We have established the, structures of an enzyme complex with the educt CTP and of a complex with, the product CMP-Kdo by X-ray diffraction analyses at 100 K, both at 2.6 A, resolution. The N-terminal domains of the dimeric enzyme bind CTP in a, peculiar nucleotide-binding fold with the beta- and gamma-phosphates, located at the so-called "PP-loop", whereas the C-terminal domains, participate in Kdo binding and in the dimer interface. The unstable, nucleotide-sugar CMP-Kdo was produced in a crystal and stabilized by, freezing to 100 K. Its formation is accompanied by an induced fit, involving mainchain displacements in the 2 A range. The observed binding, conformations together with the amino acid conservation pattern during, evolution and the putative location of the required Mg(2+) ion suggest a, reaction pathway. The enzyme is structurally homologous to the, CMP-N-acetylneuraminic acid synthetases in all parts except for the dimer, interface. Moreover, the chainfold and the substrate-binding positions, resemble those of other enzymes processing nucleotide sugars.
<StructureSection load='1gqc' size='340' side='right'caption='[[1gqc]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1gqc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GQC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GQC FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=CMK:CYTIDINE+5-MONOPHOSPHATE+3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC+ACID'>CMK</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1gqc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gqc OCA], [https://pdbe.org/1gqc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gqc RCSB], [https://www.ebi.ac.uk/pdbsum/1gqc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gqc ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KPSU5_ECOLX KPSU5_ECOLX] Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gq/1gqc_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1gqc ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The activation of the sugar 2-keto-3-deoxy-manno-octonic acid (Kdo) is catalyzed by CMP-Kdo synthetase (EC 2.7.7.38) and results in a monophosphate diester with CMP. The enzyme is a pharmaceutical target because CMP-Kdo is required for the biosynthesis of lipopolysaccharides that are vital for Gram-negative bacteria. We have established the structures of an enzyme complex with the educt CTP and of a complex with the product CMP-Kdo by X-ray diffraction analyses at 100 K, both at 2.6 A resolution. The N-terminal domains of the dimeric enzyme bind CTP in a peculiar nucleotide-binding fold with the beta- and gamma-phosphates located at the so-called "PP-loop", whereas the C-terminal domains participate in Kdo binding and in the dimer interface. The unstable nucleotide-sugar CMP-Kdo was produced in a crystal and stabilized by freezing to 100 K. Its formation is accompanied by an induced fit involving mainchain displacements in the 2 A range. The observed binding conformations together with the amino acid conservation pattern during evolution and the putative location of the required Mg(2+) ion suggest a reaction pathway. The enzyme is structurally homologous to the CMP-N-acetylneuraminic acid synthetases in all parts except for the dimer interface. Moreover, the chainfold and the substrate-binding positions resemble those of other enzymes processing nucleotide sugars.


==About this Structure==
Catalytic mechanism of CMP:2-keto-3-deoxy-manno-octonic acid synthetase as derived from complexes with reaction educt and product.,Jelakovic S, Schulz GE Biochemistry. 2002 Jan 29;41(4):1174-81. PMID:11802716<ref>PMID:11802716</ref>
1GQC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG, CMK and C5P as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] Structure known Active Site: CMK. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1GQC OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Catalytic mechanism of CMP:2-keto-3-deoxy-manno-octonic acid synthetase as derived from complexes with reaction educt and product., Jelakovic S, Schulz GE, Biochemistry. 2002 Jan 29;41(4):1174-81. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11802716 11802716]
</div>
[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]
<div class="pdbe-citations 1gqc" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Jelakovic, S.]]
[[Category: Jelakovic S]]
[[Category: Schulz, G.E.]]
[[Category: Schulz GE]]
[[Category: C5P]]
[[Category: CMK]]
[[Category: MG]]
[[Category: cmp-kdo synthetase]]
[[Category: lipopolysaccharide biosynthesis]]
[[Category: nucleoside monophosphate glycosides]]
[[Category: nucleotidyltransferase]]
[[Category: sugar-activating enzymes]]
 
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Retrieved from "https://proteopedia.org/1gqc"