We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

3vgp

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (AF_0329) from Archaeoglobus fulgidus

Structural highlights

3vgp is a 1 chain structure with sequence from Archaeoglobus fulgidus DSM 4304. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.75Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AGLB1_ARCFU Oligosaccharyl transferase (OST) that catalyzes the initial transfer of a defined glycan (a GalNAc-linked heptasaccharide composed of 4 Hex, 3 dHex and a sulfate for A.fulgidus AglB-S) from the lipid carrier dolichol-monophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation.^[1]

Publication Abstract from PubMed

Protein N-glycosylation occurs in the three domains of life. Oligosaccharyltransferase (OST) transfers glycan to asparagine in the N-glycosylation sequon. The catalytic subunit of OST is called STT3 in eukaryotes, AglB in archaea, and PglB in eubacteria. The genome of a hyperthermophilic archaeon, Archaeoglobus fulgidus, encodes three AglB paralogs. Two of them are the shortest AglBs across all domains of life. We determined the crystal structure of the C-terminal globular domain of the smallest AglB to identify the minimal structural unit. The Archaeoglobus AglB lacked a beta-barrel-like structure, which had been found in other AglB and PglB structures. In agreement, the deletion in a larger Pyrococcus AglB confirmed its dispensability for the activity. By contrast, the Archaeoglobus AglB contains a kinked helix bearing a conserved motif, called DK/MI motif. The lysine and isoleucine residues in the motif participate in the Ser/Thr recognition in the sequon. The Archaeoglobus AglB structure revealed that the kinked helix contained an unexpected insertion. A revised sequence alignment based on this finding identified a variant type of the DK motif with the insertion. A mutagenesis study of the Archaeoglobus AglB confirmed the contribution of this particular type of the DK motif to the activity. When taken together with our previous results, this study defined the classification of OST: one group consisting of eukaryotes and most archaea possesses the DK-type Ser/Thr pocket, and the other group consisting of eubacteria and the remaining archaea possesses the MI-type Ser/Thr pocket. This classification provides a useful framework for OST studies.

Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75 A Resolution.,Matsumoto S, Igura M, Nyirenda J, Matsumoto M, Yuzawa S, Noda N, Inagaki F, Kohda D Biochemistry. 2012 May 22;51(20):4157-66. Epub 2012 May 14. PMID:22559858^[2]

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

References

↑ Taguchi Y, Fujinami D, Kohda D. Comparative Analysis of Archaeal Lipid-linked Oligosaccharides That Serve as Oligosaccharide Donors for Asn Glycosylation. J Biol Chem. 2016 May 20;291(21):11042-54. PMID:27015803 doi:10.1074/jbc.M115.713156
↑ Matsumoto S, Igura M, Nyirenda J, Matsumoto M, Yuzawa S, Noda N, Inagaki F, Kohda D. Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75 A Resolution. Biochemistry. 2012 May 22;51(20):4157-66. Epub 2012 May 14. PMID:22559858 doi:10.1021/bi300076u

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3vgp"

@@ Line 3: / Line 3: @@
 <StructureSection load='3vgp' size='340' side='right'caption='[[3vgp]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3vgp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VGP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3vgp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VGP FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 1.75&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AF_0329 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dolichyl-diphosphooligosaccharide--protein_glycotransferase Dolichyl-diphosphooligosaccharide--protein glycotransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.18 2.4.99.18] </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=3vgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vgp OCA], [https://pdbe.org/3vgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vgp RCSB], [https://www.ebi.ac.uk/pdbsum/3vgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vgp ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AGLB1_ARCFU AGLB1_ARCFU] Oligosaccharyl transferase (OST) that catalyzes the initial transfer of a defined glycan (a GalNAc-linked heptasaccharide composed of 4 Hex, 3 dHex and a sulfate for A.fulgidus AglB-S) from the lipid carrier dolichol-monophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation.<ref>PMID:27015803</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Arcfu]]
+[[Category: Archaeoglobus fulgidus DSM 4304]]
-[[Category: Dolichyl-diphosphooligosaccharide--protein glycotransferase]]
 [[Category: Large Structures]]
-[[Category: Igura, M]]
+[[Category: Igura M]]
-[[Category: Inagaki, F]]
+[[Category: Inagaki F]]
-[[Category: Kohda, D]]
+[[Category: Kohda D]]
-[[Category: Matsumoto, S]]
+[[Category: Matsumoto S]]
-[[Category: Noda, N N]]
+[[Category: Noda NN]]
-[[Category: Nyirenda, J]]
+[[Category: Nyirenda J]]
-[[Category: Yuzawa, S]]
+[[Category: Yuzawa S]]
-[[Category: Cell membrane]]
-[[Category: Glycosyltransferase]]
-[[Category: Transferase]]

3vgp

From Proteopedia

Current revision

Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (AF_0329) from Archaeoglobus fulgidus

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox