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.


5bxt

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (16:05, 8 November 2023) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==LNBase in complex with LNB-NHAcAUS==
==LNBase in complex with LNB-NHAcAUS==
-
<StructureSection load='5bxt' size='340' side='right' caption='[[5bxt]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+
<StructureSection load='5bxt' size='340' side='right'caption='[[5bxt]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5bxt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BXT FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5bxt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_bifidum_JCM_1254 Bifidobacterium bifidum JCM 1254]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BXT FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4WS:N-{[(1R,2R,3R,7S,7AR)-1,2,7-TRIHYDROXYHEXAHYDRO-1H-PYRROLIZIN-3-YL]METHYL}ACETAMIDE'>4WS</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5bxp|5bxp]], [[5bxs|5bxs]], [[5bxr|5bxr]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4WS:N-{[(1R,2R,3R,7S,7AR)-1,2,7-TRIHYDROXYHEXAHYDRO-1H-PYRROLIZIN-3-YL]METHYL}ACETAMIDE'>4WS</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lacto-N-biosidase Lacto-N-biosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.140 3.2.1.140] </span></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=5bxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bxt OCA], [https://pdbe.org/5bxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bxt RCSB], [https://www.ebi.ac.uk/pdbsum/5bxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bxt ProSAT]</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=5bxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bxt OCA], [http://pdbe.org/5bxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bxt RCSB], [http://www.ebi.ac.uk/pdbsum/5bxt PDBsum]</span></td></tr>
+
</table>
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/LNBB_BIFB1 LNBB_BIFB1] Present in the infant gut, this enzyme is involved in the assimilation of type-1 human milk oligosaccharides (HMOs). It hydrolyzes via a retaining mechanism the beta-D-GlcNAc-(1->3)-beta-D-Gal linkage in lacto-N-tetraose (LNT or beta-D-Gal-(1->3)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc), an abundant HMO unique to human breast milk, releasing lacto-N-biose (LNB or beta-D-Gal-(1->3)-D-GlcNAc) and lactose (PubMed:18469123, PubMed:23479733). Is a key enzymatic factor for growth and proliferation of B.bifidum in the gut ecosystem of breast-fed infants (Probable). Has substrate preference for unmodified beta-linked LNB since it does not hydrolyze the fucosylated forms of lacto-N-tetraose (lacto-N-fucopentaose I and II) or lacto-N-neotetraose. Is also able to display transglycosylation activity in vitro (PubMed:18469123).<ref>PMID:18469123</ref> <ref>PMID:23479733</ref> <ref>PMID:23479733</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 21: Line 23:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Lacto-N-biosidase]]
+
[[Category: Bifidobacterium bifidum JCM 1254]]
-
[[Category: Arakawa, T]]
+
[[Category: Large Structures]]
-
[[Category: Fushinobu, S]]
+
[[Category: Arakawa T]]
-
[[Category: Ito, T]]
+
[[Category: Fushinobu S]]
-
[[Category: Distal gut]]
+
[[Category: Ito T]]
-
[[Category: Human milk oligosaccharide]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Inhibitor]]
+
-
[[Category: Tim barrel]]
+

Current revision

LNBase in complex with LNB-NHAcAUS

PDB ID 5bxt

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/5bxt"
Personal tools