The crystal structure of rubisco from Alcaligenes eutrophus reveals a novel central eight-stranded β-barrel formed by β-strands from four subunits

Hansen, S.B.; Vollan, Valentina Burkow; Hough, Edward; Andersen, Κjell

doi:10.1006/jmbi.1999.2701

Cited by 42 publications

(36 citation statements)

References 42 publications

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“…Thus, methylation of Cys-369 may also serve a function unique to green-algal Rubisco. None of the species for which Rubisco crystal structures have been solved contains Cys at residue positions 256 or 369 (12)(13)(14)(15)(16).…”

Section: Discussionmentioning

confidence: 99%

“…Among higher plant enzymes, the structures for Spinacia (11,12) and Nicotiana (13) Rubisco are known. Structures from the cyanobacterium Synechococcus (14), the ␤-proteobacterium Alcaligenes eutrophus (15), and the red alga Galdieria partita (16) have also been determined. Between these species, the primary and tertiary structures of the L subunits are highly similar.…”

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confidence: 99%

“…In particular, the loop between ␤ strands A and B is 12 or more residues longer in green plants than in other organisms, and the C terminus is about 30 residues longer in some of these organisms than in green plants. In Alcaligenes and Galdieria Rubisco (15,16), the longer C terminus forms a ␤-hairpin structure that extends down into the central cavity of the hexadecamer. 4-Fold local symmetry generates an eight-stranded ␤-barrel.…”

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confidence: 99%

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First Crystal Structure of Rubisco from a Green Alga,Chlamydomonas reinhardtii

Taylor

Backlund

Björhall

et al. 2001

Journal of Biological Chemistry

101

125

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The crystal structure of Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) from the unicellular green alga Chlamydomonas reinhardtii has been determined to 1.4 Å resolution. Overall, the structure shows high similarity to the previously determined structures of L8S8 Rubisco enzymes. The largest difference is found in the loop between ␤ strands A and B of the small subunit (␤A-␤B loop), which is longer by six amino acid residues than the corresponding region in Rubisco from Spinacia. Mutations of residues in the ␤A-␤B loop have been shown to affect holoenzyme stability and catalytic properties. The information contained in the Chlamydomonas structure enables a more reliable analysis of the effect of these mutations. No electron density was observed for the last 13 residues of the small subunit, which are assumed to be disordered in the crystal. Because of the high resolution of the data, some posttranslational modifications are unambiguously apparent in the structure. These include cysteine and N-terminal methylations and proline 4-hydroxylations.Ribulose 1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39; Rubisco) 1 catalyzes the addition of CO 2 to RuBP (reviewed in Refs. 1-3). This reaction initiates photosynthetic carbon assimilation via the Calvin cycle and results in the net gain of carbon from atmospheric CO 2 into the biosphere. The carboxylation reaction of Rubisco is the major source of carbon needed for life. A competing reaction in which O 2 is added to RuBP results ultimately in a net loss of CO 2 , a process known as photorespiration. Because the reaction catalyzed by Rubisco is unique to photosynthetic CO 2 fixation and nearly all carbohydrate production is dependent on it, the oxygenase reaction qualifies as the most important limiting factor of photosynthetic yield.All Rubisco enzymes have oxygenase activity. This is true also for strictly anaerobic microbes, including some anaerobic archaebacteria (reviewed in Ref. 1). Thus, whereas the ratio of carboxylation to oxygenation at any specified concentrations of CO 2 and O 2 depends on the catalytic efficiency (k cat /K m ) of carboxylation relative to that of oxygenation, referred to as the CO 2 /O 2 specificity factor, net CO 2 fixation is determined by the difference between the rates of carboxylation and oxygenation (4, 5). The kinetic constants that determine carboxylation and oxygenation vary considerably among Rubisco enzymes from different species (6).Based on their quaternary structures, different forms of Rubisco enzymes can be distinguished (reviewed in Refs. 1 and 2). In cyanobacteria and plants with chloroplasts, such as red and brown algae and green plants, a hexadecameric (L8S8) form is found, consisting of eight 55-kDa L subunits and eight 15-kDa S subunits. A dimeric (L2) enzyme, similar in structure to the L subunits of the hexadecameric enzymes, is restricted to some bacteria and alveolates. More recently, a third form was discovered in the thermophilic archaebacterium Thermococcus kodakaraensis that comprises 10 L sub...

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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First Crystal Structure of Rubisco from a Green Alga,Chlamydomonas reinhardtii

Taylor

Backlund

Björhall

et al. 2001

Journal of Biological Chemistry

101

125

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“…The S. acidophilus small subunit was phylogenetically most closely related to those from organisms with red-type algal and bacterial small subunits ( Fig. 3b) and, like those, it has an extended Cterminal region that could augment interaction with the large subunit (Hansen et al, 1999;Sugawara et al, 1999). The cbbX-encoded protein, which might be required for synthesis of active red-type RuBisCOs (Gibson & Tabita, 1997;Bowien & Kusian, 2002), differed in only one sequence position of those described as invariant when similar sequences were first compared (Gibson & Tabita, 1997).…”

Section: Substrate Affinities Of Partially Purified Rubiscosmentioning

confidence: 95%

Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species

2007

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The Calvin-Benson-Bassham (CBB) cycle has been extensively studied in proteobacteria, cyanobacteria, algae and plants, but hardly at all in Gram-positive bacteria. Some characteristics of ribulose bisphosphate carboxylase/oxygenase (RuBisCO) and a cluster of potential CBB cycle genes in a Gram-positive bacterium are described in this study with two species of Sulfobacillus (Gram-positive, facultatively autotrophic, mineral sulfide-oxidizing acidophiles). In contrast to the Gram-negative, iron-oxidizing acidophile Acidithiobacillus ferrooxidans, Sulfobacillus thermosulfidooxidans grew poorly autotrophically unless the CO 2 concentration was enhanced over that in air. However, the RuBisCO of each organism showed similar affinities for CO 2 and for ribulose 1,5-bisphosphate, and similar apparent derepression of activity under CO 2 limitation. The red-type, form I RuBisCO of Sulfobacillus acidophilus was confirmed as closely related to that of the anoxygenic phototroph Oscillochloris trichoides. Eight genes potentially involved in the CBB cycle in S. acidophilus were clustered in the order cbbA, cbbP, cbbE, cbbL, cbbS, cbbX, cbbG and cbbT.

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“…4), which also contributes residues to the active site and may contain the primary site of interaction with Rubisco activase (13,14). In the absence of RuBP or CABP, the carboxyl terminus is disordered, and loop 6 is usually disordered or misfolded into an open conformation depending on the source or treatment of the Rubisco used for crystallization (15)(16)(17)(18)(19). An open crystal structure of tobacco Rubisco was solved in which phosphate was observed to reside at a site normally occupied by the carboxyl group of Asp-473 in the closed structure (18).…”

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confidence: 99%

Substitutions at the Asp-473 Latch Residue of Chlamydomonas Ribulosebisphosphate Carboxylase/Oxygenase Cause Decreases in Carboxylation Efficiency and CO2/O2 Specificity

Satagopan

Spreitzer

2004

Journal of Biological Chemistry

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The loop between ␣-helix 6 and ␤-strand 6 in the ␣/␤-barrel active site of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1.39) plays a key role in discriminating between gaseous substrates CO 2 and O 2 . Based on numerous x-ray crystal structures, loop 6 is either closed or open depending on the presence or absence, respectively, of substrate ligands. The carboxyl terminus folds over loop 6 in the closed conformation, prompting speculation that it may trigger or latch loop 6 closure. Because an x-ray crystal structure of tobacco Rubisco revealed that phosphate is located at a site in the open form that is occupied by the carboxyl group of Asp-473 in the closed form, it was proposed that Asp-473 may serve as the latch that holds the carboxyl terminus over loop 6. To assess the essentiality of Asp-473 in catalysis, we used directed mutagenesis and chloroplast transformation of the green alga Chlamydomonas reinhardtii to create D473A and D473E mutant enzymes. The D473A and D473E mutant strains can grow photoautotrophically, indicating that Asp-473 is not essential for catalysis. However, both substitutions caused 87% decreases in carboxylation catalytic efficiency (V max /K m ) and ϳ16% decreases in CO 2 /O 2 specificity. If the carboxyl terminus is required for stabilizing loop 6 in the closed conformation, there must be additional residues at the carboxyl terminus/loop 6 interface that contribute to this mechanism. Considering that substitutions at residue 473 can influence CO 2 /O 2 specificity, further study of interactions between loop 6 and the carboxyl terminus may provide clues for engineering an improved Rubisco.Like many ␣/␤-barrel-domain enzymes (1), the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, 1 EC 4.1.1.30) has a loop (i.e. between ␤-strand 6 and ␣-helix 6) that folds over substrate during catalysis (reviewed in Refs. 2-4). Numerous studies have indicated that loop 6 plays a major role in discriminating between CO 2 and O 2 in the competing RuBP carboxylation and oxygenation reactions of Rubisco (reviewed in Refs. 2 and 3), and Lys-334 at the apex of loop 6 interacts with the C-2 carboxyl group of the transition state analog CABP in various Rubisco x-ray crystal structures (5-9). However, Rubisco may be unique among ␣/␤-barrel enzymes in that the carboxyl terminus folds over loop 6 and appears to stabilize its closed conformation. This arrangement of loop 6 and the carboxyl terminus is also observed in the crystal structure of unactivated Rubisco that contains RuBP in the active site (10). In vivo, Rubisco activase is responsible for facilitating the opening of the closed structure to release this RuBP (reviewed in Refs. 2 and 11), thereby allowing spontaneous carbamylation of an active site Lys-201 and introduction of Mg 2ϩ to produce the active form of the enzyme (reviewed in Ref. 12). The change from closed to open conformation in the carboxyl-terminal, ␣/␤-barrel domain of the large subunit is accompanied by movement of the amino-terminal domain ...

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The crystal structure of rubisco from Alcaligenes eutrophus reveals a novel central eight-stranded β-barrel formed by β-strands from four subunits

Cited by 42 publications

References 42 publications

First Crystal Structure of Rubisco from a Green Alga,Chlamydomonas reinhardtii

First Crystal Structure of Rubisco from a Green Alga,Chlamydomonas reinhardtii

Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species

Substitutions at the Asp-473 Latch Residue of Chlamydomonas Ribulosebisphosphate Carboxylase/Oxygenase Cause Decreases in Carboxylation Efficiency and CO2/O2 Specificity

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