PDBsum entry 1uzh

Lyase

PDB id: 1uzh

Contents

Protein chains

(+ 2 more) 465 a.a. *

(+ 2 more) 122 a.a. *

Ligands

CAP ×8

EDO ×50

Metals

_MG ×8

Waters ×2831

* Residue conservation analysis

PDB id:

1uzh

Name:

Lyase

Title:

A chimeric chlamydomonas, synechococcus rubisco enzyme

Structure:

Ribulose bisphosphate carboxylase large chain. Chain: a, b, e, h, k, o, r, v. Synonym: rubisco large subunit, ribulose-1,5 bisphosphate carboxylase large chain. Engineered: yes. Ribulose bisphosphate carboxylase small chain 2, ribulose bisphosphate carboxylase small chain. Chain: c, f, i, j, m, p, t, w. Synonym: rubisco small subunit 1,chloroplast, rubisco small subunit

Source:

Chlamydomonas reinhardtii, synechococcus sp. Organism_taxid: 3055, 1131. Expressed in: chlamydomonas reinhardtii, synechococcus sp. Expression_system_taxid: 3055, 1131. Chlamydomonas reinhardtii. Organism_taxid: 3055. Expressed in: chlamydomonas reinhardtii. Expression_system_taxid: 3055

Biol. unit:

60mer (from PDB file)

Resolution:

2.20Å R-factor: 0.162 R-free: 0.193

Authors:

S.Karkehabadi,R.J.Spreitzer,I.Andersson

Key ref:

S.Karkehabadi et al. (2005). Chimeric small subunits influence catalysis without causing global conformational changes in the crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase. Biochemistry, 44, 9851-9861. PubMed id: 16026157 DOI: 10.1021/bi050537v

Date:

12-Mar-04 Release date: 31-May-05

Protein chains

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

Seq: 475 a.a.

Struc: 465 a.a.*

Protein chains

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

Seq: 185 a.a.

Struc: 122 a.a.*

Protein chains

P04716  (RBS_SYNP6) -  Ribulose bisphosphate carboxylase small subunit from Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)

Seq: 111 a.a.

Struc: 122 a.a.*

* PDB and UniProt seqs differ at 62 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, E, H, K, O, R, V: 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

DOI no: 10.1021/bi050537v

Biochemistry 44:9851-9861 (2005)

PubMed id: 16026157

Chimeric small subunits influence catalysis without causing global conformational changes in the crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase.

S.Karkehabadi, S.R.Peddi, M.Anwaruzzaman, T.C.Taylor, A.Cederlund, T.Genkov, I.Andersson, R.J.Spreitzer.

ABSTRACT

Comparison of subunit sequences and X-ray crystal structures of ribulose-1,5-bisphosphate carboxylase/oxygenase indicates that the loop between beta-strands A and B of the small subunit is one of the most variable regions of the holoenzyme. In prokaryotes and nongreen algae, the loop contains 10 residues. In land plants and green algae, the loop is comprised of approximately 22 and 28 residues, respectively. Previous studies indicated that the longer betaA-betaB loop was required for the assembly of cyanobacterial small subunits with plant large subunits in isolated chloroplasts. In the present study, chimeric small subunits were constructed by replacing the loop of the green alga Chlamydomonas reinhardtii with the sequences of Synechococcus or spinach. When these engineered genes were transformed into a Chlamydomonas mutant that lacks small-subunit genes, photosynthesis-competent colonies were recovered, indicating that loop size is not essential for holoenzyme assembly. Whereas the Synechococcus loop causes decreases in carboxylation V(max), K(m)(O(2)), and CO(2)/O(2) specificity, the spinach loop causes complementary decreases in carboxylation V(max), K(m)(O(2)), and K(m)(CO(2)) without a change in specificity. X-ray crystal structures of the engineered proteins reveal remarkable similarity between the introduced betaA-betaB loops and the respective loops in the Synechococcus and spinach enzymes. The side chains of several large-subunit residues are altered in regions previously shown by directed mutagenesis to influence CO(2)/O(2) specificity. Differences in the catalytic properties of divergent Rubisco enzymes may arise from differences in the small-subunit betaA-betaB loop. This loop may be a worthwhile target for genetic engineering aimed at improving photosynthetic CO(2) fixation.