3NV6

Crystal Structure of Camphor-Bound CYP101D2

Summary for 3NV6

• Entry DOI: 10.2210/pdb3nv6/pdb
• Related: 3NV5
• Descriptor: Cytochrome P450, PROTOPORPHYRIN IX CONTAINING FE, CAMPHOR, ... (5 entities in total)
• Functional Keywords: cytochrome p450 fold, oxidizing camphor, oxidoreductase
• Biological source: Novosphingobium aromaticivorans
• Total number of polymer chains: 1
• Total formula weight: 51674.52

Authors

Yang, W.,Bell, S.G.,Wang, H.,Zhou, W.H.,Bartlam, M.,Wong, L.L.,Rao, Z. (deposition date: 2010-07-08, release date: 2010-11-03, Last modification date: 2023-11-01)

Primary citation

Yang, W.,Bell, S.G.,Wang, H.,Zhou, W.,Bartlam, M.,Wong, L.L.,Rao, Z.
The structure of CYP101D2 unveils a potential path for substrate entry into the active site
Biochem.J., 433:85-93, 2011

PubMed Abstract: The cytochrome P450 CYP101D2 from Novosphingobium aromaticivorans DSM12444 is closely related to CYP101D1 from the same bacterium and to P450cam (CYP101A1) from Pseudomonas putida. All three are capable of oxidizing camphor stereoselectively to 5-exo-hydroxycamphor. The crystal structure of CYP101D2 revealed that the likely ferredoxin-binding site on the proximal face is largely positively charged, similar to that of CYP101D1. However, both the native and camphor-soaked forms of CYP101D2 had open conformations with an access channel. In the active site of the camphor-soaked form, the camphor carbonyl interacted with the haem-iron-bound water. Two other potential camphor-binding sites were also identified from electron densities in the camphor-soaked structure: one located in the access channel, flanked by the B/C and F/G loops and the I helix, and the other in a cavity on the surface of the enzyme near the F helix side of the F/G loop. The observed open structures may be conformers of the CYP101D2 enzyme that enable the substrate to enter the buried active site via a conformational selection mechanism. The second and third binding sites may be intermediate locations of substrate entry and translocation into the active site, and provide insight into a multi-step substrate-binding mechanism.

PubMed: 20950270
DOI: 10.1042/BJ20101017

Experimental method

X-RAY DIFFRACTION (2.2 Å)