PDBsum entry 1geh

Lyase

PDB id: 1geh

Contents

Protein chains

427 a.a.

Ligands

SO4 ×10

PDB id:

1geh

Name:

Lyase

Title:

Crystal structure of archaeal rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase)

Structure:

Ribulose-1,5-bisphosphate carboxylase/oxygenase. Chain: a, b, c, d, e. Engineered: yes

Source:

Thermococcus kodakarensis. Organism_taxid: 69014. Strain: kod1. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Decamer (from PDB file)

Resolution:

2.80Å R-factor: 0.224 R-free: 0.254

Authors:

K.Kitano,N.Maeda,T.Fukui,H.Atomi,T.Imanaka,K.Miki

Key ref:

K.Kitano et al. (2001). Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry. Structure, 9, 473-481. PubMed id: 11435112 DOI: 10.1016/S0969-2126(01)00608-6

Date:

13-Nov-00 Release date: 19-Dec-01

Protein chains

O93627  (RBL_THEKO) -  Ribulose bisphosphate carboxylase from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

Seq: 444 a.a.

Struc: 427 a.a.

Enzyme reactions

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

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

Added reference

DOI no: 10.1016/S0969-2126(01)00608-6

Structure 9:473-481 (2001)

PubMed id: 11435112

Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry.

K.Kitano, N.Maeda, T.Fukui, H.Atomi, T.Imanaka, K.Miki.

ABSTRACT

BACKGROUND: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the key enzyme of the Calvin-Benson cycle and catalyzes the primary reaction of CO2 fixation in plants, algae, and bacteria. Rubiscos have been so far classified into two types. Type I is composed of eight large subunits (L subunits) and eight small subunits (S subunits) with tetragonal symmetry (L8S8), but type II is usually composed only of two L subunits (L2). Recently, some genuinely active Rubiscos of unknown physiological function have been reported from archaea. RESULTS: The crystal structure of Rubisco from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (Tk-Rubisco) was determined at 2.8 A resolution. The enzyme is composed only of L subunits and showed a novel (L2)5 decameric structure. Compared to previously known type I enzymes, each L2 dimer is inclined approximately 16 degrees to form a toroid-shaped decamer with its unique L2-L2 interfaces. Differential scanning calorimetry (DSC), circular dichroism (CD), and gel permeation chromatography (GPC) showed that Tk-Rubisco maintains its secondary structure and decameric assembly even at high temperatures. CONCLUSIONS: The present study provides the first structure of an archaeal Rubisco, an unprecedented (L2)5 decamer. Biochemical studies indicate that Tk-Rubisco maintains its decameric structure at high temperatures. The structure is distinct from type I and type II Rubiscos and strongly supports that Tk-Rubisco should be classified as a novel type III Rubisco.

Selected figure(s)

Figure 4.
Figure 4. Oligomeric Structures of Rubiscos(a) Decamer structure of Tk-Rubisco, with ribbon diagram from top view. Each monomer is shown in different colors and labeled from "A" to "J." Plausible structures of RuBP molecules and magnesium ions are marked in ellipses.(b) Side view of Tk-Rubisco by -90° rotation from (a), with the AB dimer at the center.(c) The (L[2])[4] core of type I Rubisco, with ribbon diagram from top view, where only L subunits in the L[8]S[8] structure [11] are shown. Each monomer is shown in different colors. RuBP molecules and magnesium ions are marked in ellipses.(d) Side view of the (L[2])[4] core of type I Rubisco by -90° rotation from (c)

The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 473-481) copyright 2001.

Figure was selected by the author.