4ZM3 | pdb_00004zm3

Crystal structure of PLP-Dependent 3-Aminobenzoate Synthase PctV wild-type

• PDB DOI: https://doi.org/10.2210/pdb4ZM3/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces pactum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-02 Released: 2015-10-14 
• Deposition Author(s): Hirayama, A., Miyanaga, A., Kudo, F., Eguchi, T.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.222 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Mechanism-Based Trapping of the Quinonoid Intermediate by Using the K276R Mutant of PLP-Dependent 3-Aminobenzoate Synthase PctV in the Biosynthesis of Pactamycin.

Hirayama, A., Miyanaga, A., Kudo, F., Eguchi, T.

(2015) Chembiochem 16: 2484-2490

• PubMed: 26426567 
• DOI: https://doi.org/10.1002/cbic.201500426
• Primary Citation Related Structures: 
  4ZM3, 4ZM4


• PubMed Abstract: 
  

  Mutational analysis of the pyridoxal 5'-phosphate (PLP)-dependent enzyme PctV was carried out to elucidate the multi-step reaction mechanism for the formation of 3-aminobenzoate (3-ABA) from 3-dehydroshikimate (3-DSA). Introduction of mutation K276R led to the accumulation of a quinonoid intermediate with an absorption maximum at 580 nm after the reaction of pyridoxamine 5'-phosphate (PMP) with 3-DSA. The chemical structure of this intermediate was supported by X-ray crystallographic analysis of the complex formed between the K276R mutant and the quinonoid intermediate. These results clearly show that a quinonoid intermediate is involved in the formation of 3-ABA. They also indicate that Lys276 (in the active site of PctV) plays multiple roles, including acid/base catalysis during the dehydration reaction of the quinonoid intermediate.

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Organizational Affiliation: 
• Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan.
Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan.
Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan. [e-mail].
Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan. [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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 200.24 kDa 
• Atom Count: 12,181 
• Modeled Residue Count: 1,541 
• Deposited Residue Count: 1,856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase	A, B, C, D	464	Streptomyces pactum	Mutation(s): 0  Gene Names: pctV, ptmT
UniProt
Find proteins for A8R0K5 (Streptomyces pactum) Explore A8R0K5  Go to UniProtKB:  A8R0K5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], F [auth B], G [auth C], I [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PGE	H [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	J [auth D], K [auth D], L [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.222 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.99	α = 90
b = 170.83	β = 98.33
c = 74.57	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
Coot	model building
ARP	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Hirayama, A., Miyanaga, A., Kudo, F., Eguchi, T.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology	Japan	22108003

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description