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. Author manuscript; available in PMC: 2019 Jul 14.
Published in final edited form as: Nat Chem Biol. 2019 Jan 14;15(3):295–303. doi: 10.1038/s41589-018-0203-4

Figure 6. Crystal structure of GenB1.

Figure 6.

(a) Overall structure of holo-GenB1 in complex with JI-20A. Schematic depiction of the GenB1 primary sequence is shown at the top. Dimeric structure with two flanking domains (green and magenta) and PLP-binding domains (yellow and light pink) are shown in ribbon presentation. The connecting loops between α9 and α10 in each monomer participating in the constitution of the active site in the other monomer are emphasized using thicker lines colored in forest and purple. The N-and C-termini are indicated in circles and secondary structure elements are labeled. Bound PLPs are represented by white sticks. The active site of molecule A is highlighted by a dashed circle. (b) Surface representation of the active site (left) and its schematic diagram with dimensions (right). Bound JI-20A is depicted as a black stick model and its individual sugar rings are marked as Ι, ΙΙ, and ΙΙΙ. (c–e) Close-up views of R1-, R2-, and R3-subsites. Residues constituting subsites are shown as green sticks. (c) Negatively-charged hole of the R1-subsite. The negatively-charged hole is indicated by a dashed circle in surface representation with the electrostatic potential. (d) Aromatic platform of the R2-subsite. The surfaces are colored based on the hydrophobicity of the side chains - yellow to blue representing most hydrophobic to polar side chains. The bound NM is shown as gray sticks. (e) Methyl pocket of the R3-subsite. The moieties of ring ΙΙΙ are indicated by arrows with labels.