2v69: Difference between revisions

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  {{Structure
  {{Structure
|PDB= 2v69 |SIZE=350|CAPTION= <scene name='initialview01'>2v69</scene>, resolution 2.80&Aring;
|PDB= 2v69 |SIZE=350|CAPTION= <scene name='initialview01'>2v69</scene>, resolution 2.80&Aring;
|SITE= <scene name='pdbsite=AC1:Edo+Binding+Site+For+Chain+G'>AC1</scene>
|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Cap+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Mg+Binding+Site+For+Chain+B'>AC3</scene>, <scene name='pdbsite=AC4:Cap+Binding+Site+For+Chain+B'>AC4</scene>, <scene name='pdbsite=AC5:Mg+Binding+Site+For+Chain+C'>AC5</scene>, <scene name='pdbsite=AC6:Cap+Binding+Site+For+Chain+C'>AC6</scene>, <scene name='pdbsite=AC7:Mg+Binding+Site+For+Chain+D'>AC7</scene>, <scene name='pdbsite=AC8:Cap+Binding+Site+For+Chain+D'>AC8</scene>, <scene name='pdbsite=AC9:Mg+Binding+Site+For+Chain+E'>AC9</scene>, <scene name='pdbsite=BC1:Cap+Binding+Site+For+Chain+E'>BC1</scene>, <scene name='pdbsite=BC2:Mg+Binding+Site+For+Chain+F'>BC2</scene>, <scene name='pdbsite=BC3:Cap+Binding+Site+For+Chain+F'>BC3</scene>, <scene name='pdbsite=BC4:Mg+Binding+Site+For+Chain+G'>BC4</scene>, <scene name='pdbsite=BC5:Cap+Binding+Site+For+Chain+G'>BC5</scene>, <scene name='pdbsite=BC6:Mg+Binding+Site+For+Chain+H'>BC6</scene>, <scene name='pdbsite=BC7:Cap+Binding+Site+For+Chain+H'>BC7</scene>, <scene name='pdbsite=BC8:Edo+Binding+Site+For+Chain+A'>BC8</scene>, <scene name='pdbsite=BC9:Edo+Binding+Site+For+Chain+A'>BC9</scene>, <scene name='pdbsite=CC1:Edo+Binding+Site+For+Chain+C'>CC1</scene>, <scene name='pdbsite=CC2:Edo+Binding+Site+For+Chain+C'>CC2</scene>, <scene name='pdbsite=CC3:Edo+Binding+Site+For+Chain+C'>CC3</scene>, <scene name='pdbsite=CC4:Edo+Binding+Site+For+Chain+E'>CC4</scene>, <scene name='pdbsite=CC5:Edo+Binding+Site+For+Chain+E'>CC5</scene>, <scene name='pdbsite=CC7:Edo+Binding+Site+For+Chain+G'>CC7</scene>, <scene name='pdbsite=CC8:Edo+Binding+Site+For+Chain+G'>CC8</scene>, <scene name='pdbsite=CC9:Edo+Binding+Site+For+Chain+E'>CC9</scene>, <scene name='pdbsite=DC1:Edo+Binding+Site+For+Chain+A'>DC1</scene>, <scene name='pdbsite=DC2:Edo+Binding+Site+For+Chain+H'>DC2</scene>, <scene name='pdbsite=DC3:Edo+Binding+Site+For+Chain+B'>DC3</scene>, <scene name='pdbsite=DC4:Edo+Binding+Site+For+Chain+B'>DC4</scene>, <scene name='pdbsite=DC5:Edo+Binding+Site+For+Chain+H'>DC5</scene>, <scene name='pdbsite=DC6:Edo+Binding+Site+For+Chain+H'>DC6</scene>, <scene name='pdbsite=DC7:Edo+Binding+Site+For+Chain+H'>DC7</scene>, <scene name='pdbsite=DC8:Edo+Binding+Site+For+Chain+F'>DC8</scene>, <scene name='pdbsite=DC9:Edo+Binding+Site+For+Chain+F'>DC9</scene>, <scene name='pdbsite=EC1:Edo+Binding+Site+For+Chain+D'>EC1</scene>, <scene name='pdbsite=EC2:Edo+Binding+Site+For+Chain+D'>EC2</scene>, <scene name='pdbsite=EC3:Edo+Binding+Site+For+Chain+D'>EC3</scene> and <scene name='pdbsite=EC4:Edo+Binding+Site+For+Chain+G'>EC4</scene>
|LIGAND= <scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MME:N-METHYL+METHIONINE'>MME</scene>, <scene name='pdbligand=SMC:S-METHYLCYSTEINE'>SMC</scene>
|LIGAND= <scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MME:N-METHYL+METHIONINE'>MME</scene>, <scene name='pdbligand=SMC:S-METHYLCYSTEINE'>SMC</scene>
|ACTIVITY= <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>
|ACTIVITY= <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>
|GENE=  
|GENE=  
|DOMAIN=
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=CHL00040 rbcL], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00016 RuBisCO_large], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam02788 RuBisCO_large_N], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd03527 RuBisCO_small]</span>
|RELATEDENTRY=[[1uw9|1UW9]], [[1uzh|1UZH]], [[1gk8|1GK8]], [[1ir2|1IR2]], [[1uwa|1UWA]], [[1uzd|1UZD]], [[2v63|2V63]]
|RELATEDENTRY=[[1uw9|1UW9]], [[1uzh|1UZH]], [[1gk8|1GK8]], [[1ir2|1IR2]], [[1uwa|1UWA]], [[1uzd|1UZD]], [[2v63|2V63]]
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2v69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v69 OCA], [http://www.ebi.ac.uk/pdbsum/2v69 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2v69 RCSB]</span>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2v69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v69 OCA], [http://www.ebi.ac.uk/pdbsum/2v69 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2v69 RCSB]</span>
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[[Category: transit peptide]]
[[Category: transit peptide]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:08:46 2008''
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 11:32:21 2008''

Revision as of 08:32, 2 April 2008

File:2v69.jpg


Drag the structure with the mouse to rotate
2v69, resolution 2.80Å
Sites: AC1, AC2, AC3, AC4, AC5, AC6, AC7, AC8, AC9, BC1, BC2, BC3, BC4, BC5, BC6, BC7, BC8, BC9, CC1, CC2, CC3, CC4, CC5, CC7, CC8, CC9, DC1, DC2, DC3, DC4, DC5, DC6, DC7, DC8, DC9, EC1, EC2, EC3 and EC4
Ligands: CAP, EDO, HYP, KCX, MG, MME, SMC
Activity: Ribulose-bisphosphate carboxylase, with EC number 4.1.1.39
Domains: rbcL, RuBisCO_large, RuBisCO_large_N, RuBisCO_small
Related: 1UW9, 1UZH, 1GK8, 1IR2, 1UWA, 1UZD, 2V63


Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII RUBISCO WITH A LARGE-SUBUNIT MUTATION D473E


Overview

The loop between alpha-helix 6 and beta-strand 6 in the alpha/beta-barrel of ribulose-1,5-bisphosphate carboxylase/oxygenase plays a key role in discriminating between CO2 and O2. Genetic screening in Chlamydomonas reinhardtii previously identified a loop-6 V331A substitution that decreases carboxylation and CO2/O2 specificity. Revertant selection identified T342I and G344S substitutions that restore photosynthetic growth by increasing carboxylation and specificity of the V331A enzyme. In numerous X-ray crystal structures, loop 6 is closed or open depending on the activation state of the enzyme and the presence or absence of ligands. The carboxy terminus folds over loop 6 in the closed state. To study the molecular basis for catalysis, directed mutagenesis and chloroplast transformation were used to create T342I and G344S substitutions alone. X-ray crystal structures were then solved for the V331A, V331A/T342I, T342I, and V331A/G344S enzymes, as well as for a D473E enzyme created to assess the role of the carboxy terminus in loop-6 closure. V331A disturbs a hydrophobic pocket, abolishing several van der Waals interactions. These changes are complemented by T342I and G344S, both of which alone cause decreases in CO2/O2 specificity. In the V331A/T342I revertant enzyme, Arg339 main-chain atoms are displaced. In V331A/G344S, alpha-helix 6 is shifted. D473E causes disorder of the carboxy terminus, but loop 6 remains closed. Interactions between a transition-state analogue and several residues are altered in the mutant enzymes. However, active-site Lys334 at the apex of loop 6 has a normal conformation. A variety of subtle interactions must be responsible for catalytic efficiency and CO2/O2 specificity.

About this Structure

2V69 is a Protein complex structure of sequences from Chlamydomonas reinhardtii. Full crystallographic information is available from OCA.

Reference

Structural analysis of altered large-subunit loop-6/carboxy-terminus interactions that influence catalytic efficiency and CO2/O2 specificity of ribulose-1,5-bisphosphate carboxylase/oxygenase., Karkehabadi S, Satagopan S, Taylor TC, Spreitzer RJ, Andersson I, Biochemistry. 2007 Oct 2;46(39):11080-9. Epub 2007 Sep 8. PMID:17824672

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