3kdo

From Proteopedia

(Difference between revisions)

Revision as of 07:50, 10 November 2021

Crystal structure of Type III Rubisco SP6 mutant complexed with 2-CABP

Structural highlights

3kdo is a 10 chain structure with sequence from Pyrococcus kodakaraensis (strain kod1). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Related:	1geh, 3kbn, 3a12, 3a13
Gene:	rbcL, TK2290 (Pyrococcus kodakaraensis (strain KOD1))
Activity:	Ribulose-bisphosphate carboxylase, with EC number 4.1.1.39
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RBL_THEKO] Catalyzes the addition of molecular CO(2) and H(2)O to ribulose 1,5-bisphosphate (RuBP), generating two molecules of 3-phosphoglycerate (3-PGA). Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and R15P isomerase.[HAMAP-Rule:MF_01133]^[1] ^[2] ^[3]

Publication Abstract from PubMed

The Calvin-Benson-Bassham cycle is responsible for carbon dioxide fixation in all plants, algae, and cyanobacteria. The enzyme that catalyzes the carbon dioxide-fixing reaction is ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk-Rubisco) belongs to the type III group, and shows high activity at high temperatures. We have previously found that replacement of the entire alpha-helix 6 of Tk-Rubisco with the corresponding region of the spinach enzyme (SP6 mutant) results in an improvement of catalytic performance at mesophilic temperatures, both in vivo and in vitro, whereas the former and latter half-replacements of the alpha-helix 6 (SP4 and SP5 mutants) do not yield such improvement. We report here the crystal structures of the wild-type Tk-Rubisco and the mutants SP4 and SP6, and discuss the relationships between their structures and enzymatic activities. A comparison among these structures shows the movement and the increase of temperature factors of alpha-helix 6 induced by four essential factors. We thus supposed that an increase in the flexibility of the alpha-helix 6 and loop 6 regions was important to increase the catalytic activity of Tk-Rubisco at ambient temperatures. Based on this structural information, we constructed a new mutant, SP5-V330T, which was designed to have significantly greater flexibility in the above region, and it proved to exhibit the highest activity among all mutants examined to date. The thermostability of the SP5-V330T mutant was lower than that of wild-type Tk-Rubisco, providing further support on the relationship between flexibility and activity at ambient temperatures.

Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile.,Nishitani Y, Yoshida S, Fujihashi M, Kitagawa K, Doi T, Atomi H, Imanaka T, Miki K J Biol Chem. 2010 Dec 10;285(50):39339-47. Epub 2010 Oct 6. PMID:20926376^[4]

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

References

↑ Sato T, Atomi H, Imanaka T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science. 2007 Feb 16;315(5814):1003-6. PMID:17303759 doi:http://dx.doi.org/10.1126/science.1135999
↑ Nishitani Y, Yoshida S, Fujihashi M, Kitagawa K, Doi T, Atomi H, Imanaka T, Miki K. Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile. J Biol Chem. 2010 Dec 10;285(50):39339-47. Epub 2010 Oct 6. PMID:20926376 doi:10.1074/jbc.M110.147587
↑ Ezaki S, Maeda N, Kishimoto T, Atomi H, Imanaka T. Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. J Biol Chem. 1999 Feb 19;274(8):5078-82. PMID:9988755
↑ Nishitani Y, Yoshida S, Fujihashi M, Kitagawa K, Doi T, Atomi H, Imanaka T, Miki K. Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile. J Biol Chem. 2010 Dec 10;285(50):39339-47. Epub 2010 Oct 6. PMID:20926376 doi:10.1074/jbc.M110.147587

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/3kdo"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Type III Rubisco SP6 mutant complexed with 2-CABP==
-<StructureSection load='3kdo' size='340' side='right' caption='[[3kdo]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
+<StructureSection load='3kdo' size='340' side='right'caption='[[3kdo]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kdo]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KDO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kdo]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KDO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1geh|1geh]], [[3kbn|3kbn]], [[3a12|3a12]], [[3a13|3a13]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1geh|1geh]], [[3kbn|3kbn]], [[3a12|3a12]], [[3a13|3a13]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rbcL, TK2290 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rbcL, TK2290 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </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=3kdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kdo OCA], [http://pdbe.org/3kdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kdo RCSB], [http://www.ebi.ac.uk/pdbsum/3kdo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kdo ProSAT]</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=3kdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kdo OCA], [https://pdbe.org/3kdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kdo RCSB], [https://www.ebi.ac.uk/pdbsum/3kdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kdo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RBL_THEKO RBL_THEKO]] Catalyzes the addition of molecular CO(2) and H(2)O to ribulose 1,5-bisphosphate (RuBP), generating two molecules of 3-phosphoglycerate (3-PGA). Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and R15P isomerase.[HAMAP-Rule:MF_01133]<ref>PMID:17303759</ref> <ref>PMID:20926376</ref> <ref>PMID:9988755</ref>
+[[https://www.uniprot.org/uniprot/RBL_THEKO RBL_THEKO]] Catalyzes the addition of molecular CO(2) and H(2)O to ribulose 1,5-bisphosphate (RuBP), generating two molecules of 3-phosphoglycerate (3-PGA). Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and R15P isomerase.[HAMAP-Rule:MF_01133]<ref>PMID:17303759</ref> <ref>PMID:20926376</ref> <ref>PMID:9988755</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 ==See Also==
-*[[RuBisCO|RuBisCO]]
+*[[RuBisCO 3D structures|RuBisCO 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Ribulose-bisphosphate carboxylase]]
 [[Category: Atomi, H]]

3kdo

From Proteopedia

Revision as of 07:50, 10 November 2021

Crystal structure of Type III Rubisco SP6 mutant complexed with 2-CABP

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox