3mo4: Difference between revisions

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[[Image:3mo4.jpg|left|200px]]


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==The crystal structure of an alpha-(1-3,4)-fucosidase from Bifidobacterium longum subsp. infantis ATCC 15697==
The line below this paragraph, containing "STRUCTURE_3mo4", creates the "Structure Box" on the page.
<StructureSection load='3mo4' size='340' side='right'caption='[[3mo4]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3mo4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum_subsp._infantis_ATCC_15697_=_JCM_1222_=_DSM_20088 Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MO4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MO4 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.901&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</scene></td></tr>
{{STRUCTURE_3mo4|  PDB=3mo4  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3mo4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mo4 OCA], [https://pdbe.org/3mo4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mo4 RCSB], [https://www.ebi.ac.uk/pdbsum/3mo4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mo4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/B7GNN8_BIFLS B7GNN8_BIFLS]
== 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/mo/3mo4_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3mo4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bifidobacterium longum subsp. infantis ATCC 15697 utilizes several small-mass neutral human milk oligosaccharides (HMOs), several of which are fucosylated. Whereas previous studies focused on endpoint consumption, a temporal glycan consumption profile revealed a time-dependent effect. Specifically, among preferred HMOs, tetraose was favored early in fermentation, with other oligosaccharides consumed slightly later. In order to utilize fucosylated oligosaccharides, ATCC 15697 possesses several fucosidases, implicating GH29 and GH95 alpha-L-fucosidases in a gene cluster dedicated to HMO metabolism. Evaluation of the biochemical kinetics demonstrated that ATCC 15697 expresses three fucosidases with a high turnover rate. Moreover, several ATCC 15697 fucosidases are active on the linkages inherent to the HMO molecule. Finally, the HMO cluster GH29 alpha-L-fucosidase possesses a crystal structure that is similar to previously characterized fucosidases.


===The crystal structure of an alpha-(1-3,4)-fucosidase from Bifidobacterium longum subsp. infantis ATCC 15697===
Bifidobacterium longum subsp. infantis ATCC 15697 alpha-fucosidases are active on fucosylated human milk oligosaccharides.,Sela DA, Garrido D, Lerno L, Wu S, Tan K, Eom HJ, Joachimiak A, Lebrilla CB, Mills DA Appl Environ Microbiol. 2012 Feb;78(3):795-803. Epub 2011 Dec 2. PMID:22138995<ref>PMID:22138995</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
3MO4 is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Bifidobacterium_longum_subsp._infantis Bifidobacterium longum subsp. infantis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MO4 OCA].
<div class="pdbe-citations 3mo4" style="background-color:#fffaf0;"></div>
[[Category: Bifidobacterium longum subsp. infantis]]
== References ==
[[Category: Cui, H.]]
<references/>
[[Category: Edwards, A.]]
__TOC__
[[Category: Joachimiak, A.]]
</StructureSection>
[[Category: MCSG, Midwest Center for Structural Genomics.]]
[[Category: Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088]]
[[Category: Ng, J.]]
[[Category: Large Structures]]
[[Category: Savchenko, A.]]
[[Category: Cui H]]
[[Category: Tan, K.]]
[[Category: Edwards A]]
[[Category: Xu, X.]]
[[Category: Joachimiak A]]
[[Category: Hydrolase]]
[[Category: Ng J]]
[[Category: Mcsg]]
[[Category: Savchenko A]]
[[Category: Midwest center for structural genomic]]
[[Category: Tan K]]
[[Category: Protein structure initiative]]
[[Category: Xu X]]
[[Category: Psi-2]]
[[Category: Structural genomic]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 12 11:26:04 2010''

Latest revision as of 08:59, 17 October 2024

The crystal structure of an alpha-(1-3,4)-fucosidase from Bifidobacterium longum subsp. infantis ATCC 15697The crystal structure of an alpha-(1-3,4)-fucosidase from Bifidobacterium longum subsp. infantis ATCC 15697

Structural highlights

3mo4 is a 2 chain structure with sequence from Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.901Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B7GNN8_BIFLS

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Bifidobacterium longum subsp. infantis ATCC 15697 utilizes several small-mass neutral human milk oligosaccharides (HMOs), several of which are fucosylated. Whereas previous studies focused on endpoint consumption, a temporal glycan consumption profile revealed a time-dependent effect. Specifically, among preferred HMOs, tetraose was favored early in fermentation, with other oligosaccharides consumed slightly later. In order to utilize fucosylated oligosaccharides, ATCC 15697 possesses several fucosidases, implicating GH29 and GH95 alpha-L-fucosidases in a gene cluster dedicated to HMO metabolism. Evaluation of the biochemical kinetics demonstrated that ATCC 15697 expresses three fucosidases with a high turnover rate. Moreover, several ATCC 15697 fucosidases are active on the linkages inherent to the HMO molecule. Finally, the HMO cluster GH29 alpha-L-fucosidase possesses a crystal structure that is similar to previously characterized fucosidases.

Bifidobacterium longum subsp. infantis ATCC 15697 alpha-fucosidases are active on fucosylated human milk oligosaccharides.,Sela DA, Garrido D, Lerno L, Wu S, Tan K, Eom HJ, Joachimiak A, Lebrilla CB, Mills DA Appl Environ Microbiol. 2012 Feb;78(3):795-803. Epub 2011 Dec 2. PMID:22138995[1]

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

References

  1. ↑ Sela DA, Garrido D, Lerno L, Wu S, Tan K, Eom HJ, Joachimiak A, Lebrilla CB, Mills DA. Bifidobacterium longum subsp. infantis ATCC 15697 alpha-fucosidases are active on fucosylated human milk oligosaccharides. Appl Environ Microbiol. 2012 Feb;78(3):795-803. Epub 2011 Dec 2. PMID:22138995 doi:http://dx.doi.org/10.1128/AEM.06762-11

3mo4, resolution 1.90Å

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