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4kc8

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Revision as of 18:13, 4 August 2016

Crystal Structure of Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

Structural highlights

4kc8 is a 3 chain structure with sequence from Thep1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	4kc7, 4kca, 4kcb
Gene:	Tpet_0637 (THEP1)
Activity:	Arabinan endo-1,5-alpha-L-arabinosidase, with EC number 3.2.1.99
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[EABN_THEP1] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues in different arabinan-containing polysaccharides, and releases arabinotriose and arabinobiose as end products. It acts on branched arabinan (from sugar beet), but more slowly when compared to linear or debranched arabinan.

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^[1]

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

References

↑ 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. Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases. J Biol Chem. 2014 Jan 27. PMID:24469445 doi:http://dx.doi.org/10.1074/jbc.M113.537167

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4kc8"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS==
 <StructureSection load='4kc8' size='340' side='right' caption='[[4kc8]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Tpet_0637 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=390874 THEP1])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arabinan_endo-1,5-alpha-L-arabinosidase Arabinan endo-1,5-alpha-L-arabinosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.99 3.2.1.99] </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=4kc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kc8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kc8 RCSB], [http://www.ebi.ac.uk/pdbsum/4kc8 PDBsum]</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=4kc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kc8 OCA], [http://pdbe.org/4kc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kc8 RCSB], [http://www.ebi.ac.uk/pdbsum/4kc8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kc8 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4kc8" style="background-color:#fffaf0;"></div>
 ==See Also==

4kc8

From Proteopedia

Revision as of 18:13, 4 August 2016

Crystal Structure of Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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