5Z8K | pdb_00005z8k

Crystal structure of an aminotransferase in complex with product-1

• PDB DOI: https://doi.org/10.2210/pdb5Z8K/pdb

• Classification: TRANSFERASE
• Organism(s): Micromonospora echinospora
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-31 Released: 2019-01-16 
• Deposition Author(s): Hong, S.K., Cha, S.S.
• Funding Organization(s): Ministry of Oceans and Fisheries

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Complete reconstitution of the diverse pathways of gentamicin B biosynthesis.

Ban, Y.H., Song, M.C., Hwang, J.Y., Shin, H.L., Kim, H.J., Hong, S.K., Lee, N.J., Park, J.W., Cha, S.S., Liu, H.W., Yoon, Y.J.

(2019) Nat Chem Biol 15: 295-303

• PubMed: 30643280 
• DOI: https://doi.org/10.1038/s41589-018-0203-4
• Primary Citation Related Structures: 
  5Z83, 5Z8A, 5Z8K


• PubMed Abstract: 
  

  Gentamicin B (GB), a valuable starting material for the preparation of the semisynthetic aminoglycoside antibiotic isepamicin, is produced in trace amounts by the wild-type Micromonospora echinospora. Though the biosynthetic pathway to GB has remained obscure for decades, we have now identified three hidden pathways to GB production via seven hitherto unknown intermediates in M. echinospora. The narrow substrate specificity of a key glycosyltransferase and the C6'-amination enzymes, in combination with the weak and unsynchronized gene expression of the 2'-deamination enzymes, limits GB production in M. echinospora. The crystal structure of the aminotransferase involved in C6'-amination explains its substrate specificity. Some of the new intermediates displayed similar premature termination codon readthrough activity but with reduced toxicity compared to the natural aminoglycoside G418. This work not only led to the discovery of unknown biosynthetic routes to GB, but also demonstrated the potential to mine new aminoglycosides from nature for drug discovery.

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Organizational Affiliation: 
• Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Republic of Korea.
Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, USA.
Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, Republic of Korea.
School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea.
Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Republic of Korea. [e-mail].
Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, USA. [e-mail].
Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Republic of Korea. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 95.49 kDa 
• Atom Count: 6,912 
• Modeled Residue Count: 816 
• Deposited Residue Count: 874 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-6' aminotransferase	A, B	437	Micromonospora echinospora	Mutation(s): 0  Gene Names: gacK, genB1, gntW
UniProt
Find proteins for Q70KD9 (Micromonospora echinospora) Explore Q70KD9  Go to UniProtKB:  Q70KD9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XXX (Subject of Investigation/LOI)	D [auth A], F [auth B]	(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside C12 H26 N4 O6 SYJXFKPQNSDJLI-HKEUSBCWSA-N
PLP (Subject of Investigation/LOI)	C [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.847	α = 90
b = 89.157	β = 90
c = 117.364	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Hong, S.K., Cha, S.S.

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Funding Organization	Location	Grant Number
Ministry of Oceans and Fisheries	Korea, Republic Of	20170305

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Database references
• Version 1.2: 2019-02-27
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary