Edited by Miguel De la Rosa Keywords:Family-3 carbohydrate-binding module (CBM3) Family-9 glycoside hydrolases (GH9) Cellulose Cellulase Endoglucanase a b s t r a c t Clostridium thermocellum cellulase 9I (Cel9I) is a non-cellulosomal tri-modular enzyme, consisting of a family-9 glycoside hydrolase (GH9) catalytic module and two family-3 carbohydrate-binding modules (CBM3c and CBM3b). The presence of CBM3c was previously shown to be essential for activity, however the mechanism by which it functions is unclear. We expressed the three recombinant modules independently in Escherichia coli and examined their interactions. Non-denaturing gel electrophoresis, isothermal titration calorimetry, and affinity purification of the GH9-CBM3c complex revealed a specific non-covalent binding interaction between the GH9 module and CBM3c. Their physical association was shown to recover 60-70% of the intact Cel9I endoglucanase activity.

[NiFe]-hydrogenases are multimeric proteins. The large subunit contains the NiFe(CN)(2)CO bimetallic active center and the small subunit contains Fe-S clusters. Biosynthesis and assembly of the NiFe(CN)(2)CO active center requires six Hyp accessory proteins. The synthesis of the CN(-) ligands is catalyzed by the combined actions of HypF and HypE using carbamoylphosphate as a substrate. We report the structure of Escherichia coli HypF(92-750) lacking the N-terminal acylphosphatase domain. HypF(92-750) comprises the novel Zn-finger domain, the nucleotide-binding YrdC-like domain, and the Kae1-like universal domain, also binding a nucleotide and a Zn(2+) ion. The two nucleotide-binding sites are sequestered in an internal cavity, facing each other and separated by ∼14 Å. The YrdC-like domain converts carbamoyl moiety to a carbamoyl adenylate intermediate, which is channeled to the Kae1-like domain. Mutations within either nucleotide-binding site compromise hydrogenase maturation but do not affect the carbamoylphosphate phosphatase activity.

Non-cellulosomal processive endoglucanase 9I (Cel9I) from Clostridium thermocellum is a modular protein, consisting of a family-9 glycoside hydrolase (GH9) catalytic module and two family-3 carbohydrate-binding modules (CBM3c and CBM3b), separated by linker regions. GH9 does not show cellulase activity when expressed without CBM3c and CBM3b and the presence of the CBM3c was previously shown to be essential for endoglucanase activity. Physical reassociation of independently expressed GH9 and CBM3c modules (containing linker sequences) restored 60–70% of the intact Cel9I endocellulase activity. However, the mechanism responsible for recovery of activity remained unclear. In this work we independently expressed recombinant GH9 and CBM3c with and without their interconnecting linker in Escherichia coli. We crystallized and determined the molecular structure of the GH9/linker-CBM3c heterodimer at a resolution of 1.68 Å to understand the functional and structural importance of the mutual spatial orientation of the modules and the role of the interconnecting linker during their re-association. Enzyme activity assays and isothermal titration calorimetry were performed to study and compare the effect of the linker on the re-association. The results indicated that reassembly of the modules could also occur without the linker, albeit with only very low recovery of endoglucanase activity. We propose that the linker regions in the GH9/CBM3c endoglucanases are important for spatial organization and fixation of the modules into functional enzymes.

The crystal structure of the family 3b carbohydrate‐binding module (CBM3b) of the cellulosomal multimodular hydrolytic enzyme cellobiohydrolase 9A (Cbh9A) from Clostridium thermocellum has been determined. Cbh9A CBM3b crystallized in space group P41 with four molecules in the asymmetric unit and diffracted to a resolution of 2.20 Å using synchrotron radiation. The structure was determined by molecular replacement using C. thermocellum Cel9V CBM3b′ (PDB entry http://scripts.iucr.org/cgi-bin/explore.cgi?pdbid=2wnx) as a model. The C. thermocellum Cbh9A CBM3b molecule forms a nine‐stranded antiparallel β‐sandwich similar to other family 3 carbohydrate‐binding modules (CBMs). It has a short planar array of two aromatic residues that are assumed to bind cellulose, yet it lacks the ability to bind cellulose. The molecule contains a shallow groove of unknown function that characterizes other family 3 CBMs with high sequence homology. In addition, it contains a calcium‐binding site formed by a group of amino‐acid residues that are highly conserved in similar structures. After determination of the three‐dimensional structure of Cbh9A CBM3b, the site‐specific N126W mutant was produced with the intention of enhancing the cellulose‐binding ability of the CBM. Cbh9A CBM3bN126W crystallized in space group P41212, with one molecule in the asymmetric unit. The crystals diffracted to 1.04 Å resolution using synchrotron radiation. The structure of Cbh9A CBM3bN126W revealed incorporation of the mutated Trp126 into the putative cellulose‐binding strip of residues. Cellulose‐binding experiments demonstrated the ability of Cbh9A CBM3bN126W to bind cellulose owing to the mutation. This is the first report of the engineered conversion of a non‐cellulose‐binding CBM3 to a binding CBM3 by site‐directed mutagenesis. The three‐dimensional structure of Cbh9A CBM3bN126W provided a structural correlation with cellulose‐binding ability, revealing a longer planar array of definitive cellulose‐binding residues.

Family 3 carbohydrate-binding modules (CBM3s) are associated with both cellulosomal scaffoldins and family 9 glycoside hydrolases (GH9s), which are multi-modular enzymes that act on cellulosic substrates. CBM3s bind cellulose. X-ray crystal structures of these modules have established an accepted cellulose-binding mechanism based on stacking interactions between the sugar rings of cellulose and a planar array of aromatic residues located on the CBM3 surface. These planar-strip residues are generally highly conserved, although some CBM3 sequences lack one or more of these residues. In particular, CBM3b' from Clostridium thermocellum Cel9V exhibits such sequence changes and fails to bind cellulosic substrates. A crystallographic investigation of CBM3b' has been initiated in order to understand the structural reason(s) for this inability. CBM3b' crystallized in space group C222(1) (diffraction was obtained to 2.0 A resolution in-house) with three independent molecules in the asymmetric unit and in space group P4(1)2(1)2 (diffraction was obtained to 1.79 A resolution in-house and to 1.30 A resolution at a synchrotron) with one molecule in the asymmetric unit. The molecular structure of Cel9V CBM3b' revealed that in addition to the loss of several cellulose-binding residues in the planar strip, changes in the backbone create a surface 'hump' which could interfere with the formation of cellulose-protein surface interactions and thus prevent binding to crystalline cellulose.