PDBsum entry 2v6a

Oxidoreductase

PDB id: 2v6a

Contents

Protein chains

(+ 2 more) 467 a.a. *

(+ 2 more) 140 a.a. *

Ligands

CAP ×8

EDO ×59

Metals

_MG ×8

Waters ×3492

* Residue conservation analysis

PDB id:

2v6a

Name:

Oxidoreductase

Title:

Crystal structure of chlamydomonas reinhardtii rubisco with large- subunit mutations v331a, g344s

Structure:

Ribulose bisphosphate carboxylase large chain. Chain: a, b, c, d, e, f, g, h. Synonym: ribulose-1,5-bisphosphate carboxylase large chain. Engineered: yes. Mutation: yes. Ribulose bisphosphate carboxylase small chain 1. Chain: i, j, k, l, m, n, o, p. Synonym: rubisco small subunit 1,ribulose-1,5-bisphosphate carboxylase small chain.

Source:

Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: 2137. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Resolution:

1.50Å R-factor: 0.177 R-free: 0.192

Authors:

S.Karkehabadi,S.Satagopan,T.C.Taylor,R.J.Spreitzer,I.Andersson

Key ref:

S.Karkehabadi et al. (2007). 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. Biochemistry, 46, 11080-11089. PubMed id: 17824672

Date:

14-Jul-07 Release date: 31-Jul-07

Protein chains

P00877  (RBL_CHLRE) -  Ribulose bisphosphate carboxylase large chain from Chlamydomonas reinhardtii

Seq: 475 a.a.

Struc: 467 a.a.*

Protein chains

P00873  (RBS1_CHLRE) -  Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 from Chlamydomonas reinhardtii

Seq: 185 a.a.

Struc: 140 a.a.*

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.4.1.1.39 - ribulose-bisphosphate carboxylase.
• Reaction: 2 (2R)-3-phosphoglycerate + 2 H⁺ = D-ribulose 1,5-bisphosphate + CO2 + H2O

2 × (2R)-3-phosphoglycerate + 2 × H(+) = D-ribulose 1,5-bisphosphate (Bound ligand (Het Group name = EDO) matches with 40.00% similarity) + CO2 (Bound ligand (Het Group name = CAP) matches with 85.71% similarity) + H2O

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Biochemistry 46:11080-11089 (2007)

PubMed id: 17824672

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.

S.Karkehabadi, S.Satagopan, T.C.Taylor, R.J.Spreitzer, I.Andersson.

ABSTRACT

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.