4kcb: Difference between revisions
New page: '''Unreleased structure''' The entry 4kcb is ON HOLD Authors: Santos, C.R., Polo, C.C., Costa, M.C.M.F., Nascimento, A.F.Z., Wong, D.W.S., Murakami, M.T. Description: Crystal Structure... |
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The | ==Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library== | ||
<StructureSection load='4kcb' size='340' side='right'caption='[[4kcb]], [[Resolution|resolution]] 2.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4kcb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KCB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KCB 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]] 2.9Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4kcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kcb OCA], [https://pdbe.org/4kcb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kcb RCSB], [https://www.ebi.ac.uk/pdbsum/4kcb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kcb ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/D2XML8_9BACT D2XML8_9BACT] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Arabinanases (ABNs, EC 3.2.1.99) are promising catalysts for environmental friendly biomass conversion into energy and chemicals. These enzymes catalyze the hydrolysis of the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans releasing arabino-oligosaccharides and arabinose, the second most abundant pentose in nature. In this work, new findings about the molecular mechanisms governing activation, functional differentiation and catalysis of GH43 ABNs are presented. Biophysical, mutational and biochemical studies with the hyperthermostable two-domain endo-acting ABN from Thermotoga petrophila (TpABN) revealed how some GH43 ABNs are activated by calcium ions via hyperpolarization of the catalytically-relevant histidine and the importance of the ancillary domain for catalysis and conformational stability. On the other hand, the two GH43 ABNs from rumen metagenome, ARN2 and ARN3, presented a calcium-independent mechanism in which sodium is the most likely substituent for calcium ions. The crystal structure of the two-domain endo-acting ARN2 showed that its ability to efficiently degrade branched substrates is due to a larger catalytic interface with higher accessibility than that observed in other ABNs with preference for linear arabinan. Moreover, crystallographic characterization of the single-domain exo-acting ARN3 indicated that its cleavage pattern producing arabinose is associated with the chemical recognition of reducing end of the substrate imposed by steric impediments at the aglycone-binding site. By structure-guided rational design, ARN3 was converted into a classical endo enzyme, confirming the role of the extended Arg203-Ala230 loop in determining its action mode. These results reveal novel molecular aspects concerning the functioning of GH43 ABNs and provide new strategies for arabinan degradation. | |||
Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases.,Santos CR, Polo CC, Costa MC, Nascimento AF, Meza AN, Cota J, Hoffmam ZB, Honorato RV, Oliveira PS, Goldman GH, Gilbert HJ, Prade RA, Ruller R, Squina FM, Wong DW, Murakami MT J Biol Chem. 2014 Jan 27. PMID:24469445<ref>PMID:24469445</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4kcb" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Arabinanase 3D structures|Arabinanase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Uncultured bacterium]] | |||
[[Category: Costa MCMF]] | |||
[[Category: Murakami MT]] | |||
[[Category: Nascimento AFZ]] | |||
[[Category: Polo CC]] | |||
[[Category: Santos CR]] | |||
[[Category: Wong DWS]] | |||