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3n98

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Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose and additives

Structural highlights

3n98 is a 1 chain structure with sequence from Thermococcus kodakarensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.87Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BE_THEKO Catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. The branch chain-length distribution of the reaction products shows degree of polymerization (DP) of 5 to 30, with two local maxima at DP 6 and DP 11. Exhibits an alpha-retaining catalytic mechanism. Does not display alpha-galactosidase or pullulanase activity, since melibiose and pullulan are not substrates. Is not able to catalyze the hydrolysis or transglycosylation of maltoheptaose, suggesting that the TK1436 protein contains neither alpha-amylase nor 4-alpha-glucanotransferase activity.^[1]

Publication Abstract from PubMed

Branching enzymes (BEs) catalyze the formation of branch points in glycogen and amylopectin by cleavage of alpha-1,4 glycosidic bonds and subsequent transfer to a new alpha-1,6 position. BEs generally belong to glycoside hydrolase family 13 (GH13); however TK1436, isolated from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1, is the first GH57 member, which possesses BE activity. To date, the only BE structure that had been determined is a GH13-type from Escherichia coli. Herein, we have determined the crystal structure of TK1436 in the native state and in complex with glucose and substrate mimetics that permitted mapping of the substrate-binding channel and identification of key residues for glucanotransferase activity. Its structure encompasses a distorted (beta/alpha)(7)-barrel juxtaposed to a C-terminal alpha-helical domain, which also participates in the formation of the active-site cleft. The active site comprises two acidic catalytic residues (Glu183 and Asp354), the polarizer His10, aromatic gate-keepers (Trp28, Trp270, Trp407, and Trp416) and the residue Tyr233, which is fully conserved among GH13- and GH57-type BEs. Despite TK1436 displaying a completely different fold and domain organization when compared to E. coli BE, they share the same structural determinants for BE activity. Structural comparison with AmyC, a GH57 alpha-amylase devoid of BE activity, revealed that the catalytic loop involved in substrate recognition and binding, is shortened in AmyC structure and it has been addressed as a key feature for its inability for glucanotransferase activity. The oligomerization has also been pointed out as a possible determinant for functional differentiation among GH57 members.

Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.,Santos CR, Tonoli CC, Trindade DM, Betzel C, Takata H, Kuriki T, Kanai T, Imanaka T, Arni RK, Murakami MT Proteins. 2011 Feb;79(2):547-57. PMID:21104698^[2]

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

References

↑ Murakami T, Kanai T, Takata H, Kuriki T, Imanaka T. A novel branching enzyme of the GH-57 family in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol. 2006 Aug;188(16):5915-24. PMID:16885460 doi:http://dx.doi.org/10.1128/JB.00390-06
↑ Santos CR, Tonoli CC, Trindade DM, Betzel C, Takata H, Kuriki T, Kanai T, Imanaka T, Arni RK, Murakami MT. Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Proteins. 2011 Feb;79(2):547-57. PMID:21104698 doi:10.1002/prot.22902

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/3n98"

@@ Line 3: / Line 3: @@
 <StructureSection load='3n98' size='340' side='right'caption='[[3n98]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3n98]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"thermococcus_kodakaraensis"_atomi_et_al._2004 "thermococcus kodakaraensis" atomi et al. 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N98 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N98 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3n98]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N98 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N98 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.87&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3n8t|3n8t]], [[3n92|3n92]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK1436 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311400 "Thermococcus kodakaraensis" Atomi et al. 2004])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/1,4-alpha-glucan_branching_enzyme 1,4-alpha-glucan branching enzyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.18 2.4.1.18] </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=3n98 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n98 OCA], [https://pdbe.org/3n98 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n98 RCSB], [https://www.ebi.ac.uk/pdbsum/3n98 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n98 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/BE_THEKO BE_THEKO]] Catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. The branch chain-length distribution of the reaction products shows degree of polymerization (DP) of 5 to 30, with two local maxima at DP 6 and DP 11. Exhibits an alpha-retaining catalytic mechanism. Does not display alpha-galactosidase or pullulanase activity, since melibiose and pullulan are not substrates. Is not able to catalyze the hydrolysis or transglycosylation of maltoheptaose, suggesting that the TK1436 protein contains neither alpha-amylase nor 4-alpha-glucanotransferase activity.<ref>PMID:16885460</ref>
+[https://www.uniprot.org/uniprot/BE_THEKO BE_THEKO] Catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. The branch chain-length distribution of the reaction products shows degree of polymerization (DP) of 5 to 30, with two local maxima at DP 6 and DP 11. Exhibits an alpha-retaining catalytic mechanism. Does not display alpha-galactosidase or pullulanase activity, since melibiose and pullulan are not substrates. Is not able to catalyze the hydrolysis or transglycosylation of maltoheptaose, suggesting that the TK1436 protein contains neither alpha-amylase nor 4-alpha-glucanotransferase activity.<ref>PMID:16885460</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Thermococcus kodakaraensis atomi et al. 2004]]
-[[Category: 1,4-alpha-glucan branching enzyme]]
 [[Category: Large Structures]]
-[[Category: Arni, R K]]
+[[Category: Thermococcus kodakarensis]]
-[[Category: Betzel, C]]
+[[Category: Arni RK]]
-[[Category: Imanaka, T]]
+[[Category: Betzel C]]
-[[Category: Kanai, T]]
+[[Category: Imanaka T]]
-[[Category: Kuriki, T]]
+[[Category: Kanai T]]
-[[Category: Murakami, M T]]
+[[Category: Kuriki T]]
-[[Category: Santos, C R]]
+[[Category: Murakami MT]]
-[[Category: Takata, H]]
+[[Category: Santos CR]]
-[[Category: Tonoli, C C.C]]
+[[Category: Takata H]]
-[[Category: Trindade, D M]]
+[[Category: Tonoli CCC]]
-[[Category: Branching enzyme]]
+[[Category: Trindade DM]]
-[[Category: Gh57 family member]]
-[[Category: Transferase]]

3n98

From Proteopedia

Current revision

Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose and additives

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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