7S3J

Crystal Structure of AspB P450 in complex with brevianamide F substrates

PDB DOI: https://doi.org/10.2210/pdb7S3J/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces sp. NRRL S-1868
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-09-07 Released: 2022-11-09
Deposition Author(s): Newmister, S.A., Shende, V.V., Harris, N.R., Sanders, J.N., Khatri, Y., Movassaghi, M., Houk, K.N., Sherman, D.H.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.292
R-Value Work: 0.226
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases.

Shende, V.V., Harris, N.R., Sanders, J.N., Newmister, S.A., Khatri, Y., Movassaghi, M., Houk, K.N., Sherman, D.H.

(2023) Angew Chem Int Ed Engl 62: e202210254-e202210254

PubMed: 36610039 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/anie.202210254
Primary Citation of Related Structures:
7S3J, 7S3T

PubMed Abstract:
In the biosynthesis of the tryptophan-linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high-resolution crystal structure of selective Csp ² -N bond forming dimerase, AspB. Overlay of the AspB structure onto C-C and C-N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities. Molecular dynamics (MD) simulations identified a region of NzeB with increased conformational flexibility relative to AspB, and interchange of this region along with a single active site mutation led to a variant that catalyzes exclusive C-N bond formation. MD simulations also suggest that intermolecular C-C or C-N bond formation results from a change in mechanism, supported experimentally through use of a substrate mimic.

Organizational Affiliation

Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA.

Macromolecule Content

Total Structure Weight: 90.01 kDa
Atom Count: 6,512
Modelled Residue Count: 794
Deposited Residue Count: 802
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AspB	A, B	401	Streptomyces sp. NRRL S-1868	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
QRP (Subject of Investigation/LOI) Query on QRP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B]	(3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione C₁₆ H₁₇ N₃ O₂ RYFZBPVMVYTEKZ-KBPBESRZSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.292
R-Value Work: 0.226
R-Value Observed: 0.229
Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.359	α = 90
b = 100.619	β = 92.76
c = 107.716	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1700982
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM118101