4ZM4 | pdb_00004zm4

Complex structure of PctV K276R mutant with PMP and 3-dehydroshkimate

PDB DOI: https://doi.org/10.2210/pdb4ZM4/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces pactum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.278 (Depositor), 0.283 (DCC)
R-Value Work:
0.238 (Depositor), 0.245 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan.

Macromolecule Content

Total Structure Weight: 288.8 kDa
Atom Count: 19,717
Modeled Residue Count: 2,490
Deposited Residue Count: 2,682
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase	A, B, C, D, E A, B, C, D, E, F	447	Streptomyces pactum	Mutation(s): 1 Gene Names: pctV, ptmT
UniProt
Find proteins for A8R0K5 (Streptomyces pactum) Explore A8R0K5 Go to UniProtKB: A8R0K5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8R0K5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P3B Query on P3B Download:Ideal Coordinates CCD File SDF format, chain K [auth E] SDF format, chain H [auth B] MOL2 format, chain K [auth E] MOL2 format, chain H [auth B] mmCIF format, chain K [auth E] mmCIF format, chain H [auth B]	H [auth B], K [auth E]	(3E,4R,5R)-4,5-dihydroxy-3-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}cyclohex-1-ene-1-carboxylic acid C₁₅ H₁₉ N₂ O₉ P KOPNIGHVUGDBMS-FEZKIMOASA-N		Interactions Focus chain H [auth B] Focus chain K [auth E] Interactions & Density Focus chain H [auth B] Focus chain K [auth E]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain G [auth A] MOL2 format, chain L [auth F] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth A] mmCIF format, chain L [auth F] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth A]	G [auth A], I [auth C], J [auth D], L [auth F]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.278 (Depositor), 0.283 (DCC)
R-Value Work: 0.238 (Depositor), 0.245 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.93	α = 90
b = 178.93	β = 90
c = 467.899	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

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

Revision History (Full details and data files)

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