The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica  Jonas Uppenberg, Mogens Trier Hansen, Shamkant Patkar, T.Alwyn Jones  Structure  Volume 2, Issue 4, Pages 293-308 (April 1994) DOI: 10.1016/S0969-2126(00)00031-9

Figure 1 DNA sequence of the Candida antarctica lipase B gene and the deduced amino acid sequence. Numbers refer to the amino acid position in the mature lipase. The pre-propeptide (amino acids −25 to −1, shown in italics) contains a sequence (−25 to −8) typical of signal peptides [51] and a short propeptide ending in two basic amino acids forming a possible target for KEX2 type [52] proteolytic processing into the mature protease. The position of the probes used for screening are indicated by solid lines: NOR930 (sense, line above sequence) and NOR929 (antisense; line below sequence). The active site residues are underlined with double lines and the N-glycosylation is marked with a dashed line. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 2 Stereo drawing of the Cα trace of CALB. The structure is coloured red at the amino terminus, then orange, light green, dark green, pale blue, and finally dark blue at the carboxyl terminus. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 3 Secondary structure diagram of CALB. The assignment of secondary structure was carried out with the program DSSP [53]. Helices α 2, α 9 and α 10 all have short regions where the hydrogen bonding pattern for helices is broken and the direction of the helix changes. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 4 The superposition of CALB (green), Rhizomucor miehei lipase (magenta), Geotrichum candidum lipase (red) and human pancreatic lipase (purple) around the active site serine. Only the Cα atoms of the β -strand were used in this alignment. Thr103, a buried water and Ser105 in CALB are also shown. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 5 A stereo picture showing density in a 2F obs− F calc map around the catalytic triad at 1.55 å resolution. A buried water residue is tightly associated with the catalytic residue Asp187 through a hydrogen bond. Carbon atoms are shown in green, nitrogens in purple and oxygens in red. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 6 A stereo picture of the catalytic triad residues and nearby polar residues, Asp134, Gln157 and Thr40 that form a hydrogen bonding network with the solvent in the active site cavity. Colour scheme as for Figure 5. At the top of the picture is the most likely candidate for a lid in CALB and the side chains that form stabilizing hydrogen bonds in this region. The residues that are disordered in one of the molecules of the monoclinic crystal form in the high pH structure are shown in magenta. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 7 A stereo picture of the RML-phosphonate inhibitor complex and an alignment with CALB in this region. All residues believed to make up the oxyanion hole have a similar conformation in the two enzymes. Hypothetical hydrogen bonds from the inhibitor to CALB are indicated by dashed lines. RML is shown in black, CALB in the colour scheme used for Figure 5. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 8 The active site pocket in its open conformation from the orthorhombic model. (a) View from above and (b) as a cross section. A solvent accessible surface was calculated with VOIDOO [54] using a 1 å probe radius. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 8 The active site pocket in its open conformation from the orthorhombic model. (a) View from above and (b) as a cross section. A solvent accessible surface was calculated with VOIDOO [54] using a 1 å probe radius. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 9 A 2F obs− F calc map around the N-glycosylation site in CALB in the orthorhombic crystal form. Two N-acetylglucosamine molecules have been built in the density. The average temperature factor for the carbohydrate atoms is 27 å 2 in the orthorhombic model. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 10 Plots of the real space fit for all atoms (solid lines) and average temperature factors for main chain atoms (dashed lines) of the current orthorhombic model as a function of residue number. The scale on the left shows the real-space correlation coefficient and the scale on the right shows B-factor values in å 2. For the real space fit, a 2F obs− Fcalcmap was used. All 317 residues are visible in the electron density map and have been modelled. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 11 A stereo plot of the asymmetric unit in the monoclinic crystal form at pH 3.6 showing how one molecule packs its hydrophobic surface against that of another, thereby minimizing their exposure to the surrounding solvent. Molecule A in red, molecule B in green, waters and β -octyl glucoside molecules in purple. The molecules are related by an almost exact two-fold rotation. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 12 Stereo picture of an F obs− Fcalc map around the lipid molecule, most likely β -octyl glucoside, in the monoclinic crystal form. The lipid part of the molecule points into the active site pocket of molecule A and the carbohydrate moiety forms hydrogen bonds to molecule B. The map is contoured at 2σ. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 13 Ramachandran plot of the current orthorhombic model. Two residues with unusual conformations are evident. Asn51 is located in a kinked helix, adding an extra residue to one of the turns. Ser105 has the typical conformation for the active site nucleophile found in lipases and α / β -hydrolases. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 14 Real-space fit and main chain temperature factor diagrams for the monoclinic models for both molecules in the asymmetric unit as a function of residue number. The scales on the left show the real- space correlation coefficient and the scales on the right show B- factor values in å 2. (a) Molecule A at pH 3.6. (b) Molecule B at pH 3.6. (c) Molecule A at pH 5.5. (d) Molecule B at pH 5.5. Part of the proposed lid region, helix α 5, lacks continuous density in the structure of molecule B at high pH. In this molecule, density for a lipid molecule in the active site can be seen for the low pH structure. This density disappears in the structure determined at pH 5.5. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 14 Real-space fit and main chain temperature factor diagrams for the monoclinic models for both molecules in the asymmetric unit as a function of residue number. The scales on the left show the real- space correlation coefficient and the scales on the right show B- factor values in å 2. (a) Molecule A at pH 3.6. (b) Molecule B at pH 3.6. (c) Molecule A at pH 5.5. (d) Molecule B at pH 5.5. Part of the proposed lid region, helix α 5, lacks continuous density in the structure of molecule B at high pH. In this molecule, density for a lipid molecule in the active site can be seen for the low pH structure. This density disappears in the structure determined at pH 5.5. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 14 Real-space fit and main chain temperature factor diagrams for the monoclinic models for both molecules in the asymmetric unit as a function of residue number. The scales on the left show the real- space correlation coefficient and the scales on the right show B- factor values in å 2. (a) Molecule A at pH 3.6. (b) Molecule B at pH 3.6. (c) Molecule A at pH 5.5. (d) Molecule B at pH 5.5. Part of the proposed lid region, helix α 5, lacks continuous density in the structure of molecule B at high pH. In this molecule, density for a lipid molecule in the active site can be seen for the low pH structure. This density disappears in the structure determined at pH 5.5. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)

Figure 14 Real-space fit and main chain temperature factor diagrams for the monoclinic models for both molecules in the asymmetric unit as a function of residue number. The scales on the left show the real- space correlation coefficient and the scales on the right show B- factor values in å 2. (a) Molecule A at pH 3.6. (b) Molecule B at pH 3.6. (c) Molecule A at pH 5.5. (d) Molecule B at pH 5.5. Part of the proposed lid region, helix α 5, lacks continuous density in the structure of molecule B at high pH. In this molecule, density for a lipid molecule in the active site can be seen for the low pH structure. This density disappears in the structure determined at pH 5.5. Structure 1994 2, 293-308DOI: (10.1016/S0969-2126(00)00031-9)