5ZOL | pdb_00005zol

Crystal structure of a three sites mutantion of FSAA complexed with HA and product

PDB DOI: https://doi.org/10.2210/pdb5ZOL/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-04-13 Released: 2019-06-12
Deposition Author(s): Wu, L., Yang, X.H., Yu, H.W., Zhou, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.191 (Depositor), 0.192 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The engineering of decameric d-fructose-6-phosphate aldolase A by combinatorial modulation of inter- and intra-subunit interactions.

Yang, X., Wu, L., Li, A., Ye, L., Zhou, J., Yu, H.

(2020) Chem Commun (Camb) 56: 7561-7564

PubMed: 32519699 Search on PubMed
DOI: https://doi.org/10.1039/d0cc02437f
Primary Citation Related Structures:
5ZOL

PubMed Abstract:
The combinatorial modulation of inter- and intra-subunit interactions of decameric d-fructose-6-phosphate aldolase A (FSAA) generated a triple-site variant I31T/Q59T/I195Q FSAA with 27- to 278-fold improvement in activity towards target heteroaromatic aldehydes. X-ray crystallographic data and molecular dynamics simulations ascribed the enhanced activity to the pronounced flexibility of the interface region between subunits, the expanded substrate entrance and binding pocket, and enhanced proton transfer, unambiguously demonstrating the efficiency of this strategy for engineering multimeric enzymes.

Organizational Affiliation

Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China. yuhongwei@zju.edu.cn yelidan@zju.edu.cn.

Macromolecule Content

Total Structure Weight: 272.82 kDa
Atom Count: 17,350
Modeled Residue Count: 2,212
Deposited Residue Count: 2,550
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-6-phosphate aldolase 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	255	Escherichia coli K-12	Mutation(s): 3 Gene Names: fsaA, fsa, mipB, ybiZ, b0825, JW5109 EC: 4.1.2
UniProt
Find proteins for P78055 (Escherichia coli (strain K12)) Explore P78055 Go to UniProtKB: P78055
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78055
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LW2 Query on LW2 Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain LA [auth I] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] SDF format, chain PA [auth J] SDF format, chain L [auth A] SDF format, chain IA [auth H] MOL2 format, chain BA [auth F] MOL2 format, chain LA [auth I] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain PA [auth J] MOL2 format, chain L [auth A] MOL2 format, chain IA [auth H] mmCIF format, chain BA [auth F] mmCIF format, chain LA [auth I] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain PA [auth J] mmCIF format, chain L [auth A] mmCIF format, chain IA [auth H]	BA [auth F] IA [auth H] L [auth A] LA [auth I] P [auth B] BA [auth F], IA [auth H], L [auth A], LA [auth I], P [auth B], PA [auth J], S [auth C], V [auth D], Y [auth E]	(3S,4S)-3,4-dihydroxy-4-(thiophen-2-yl)butan-2-one C₈ H₁₀ O₃ S IGRSBLNSJJCYEW-HTQZYQBOSA-N		Interactions Focus chain BA [auth F] Focus chain IA [auth H] Focus chain L [auth A] Focus chain LA [auth I] Focus chain P [auth B] Focus chain PA [auth J] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain IA [auth H] Focus chain L [auth A] Focus chain LA [auth I] Focus chain P [auth B] Focus chain PA [auth J] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]
LW1 Query on LW1 Download:Ideal Coordinates CCD File SDF format, chain FA [auth G] MOL2 format, chain FA [auth G] mmCIF format, chain FA [auth G]	FA [auth G]	thiophene-2-carbaldehyde C₅ H₄ O S CNUDBTRUORMMPA-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Interactions & Density Focus chain FA [auth G]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain GA [auth G] SDF format, chain JA [auth H] SDF format, chain N [auth A] SDF format, chain NA [auth I] SDF format, chain Q [auth B] SDF format, chain QA [auth J] SDF format, chain Z [auth E] SDF format, chain W [auth D] SDF format, chain DA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth J] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth D] MOL2 format, chain DA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth J] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth D] mmCIF format, chain DA [auth F]	DA [auth F] GA [auth G] JA [auth H] N [auth A] NA [auth I] DA [auth F], GA [auth G], JA [auth H], N [auth A], NA [auth I], Q [auth B], QA [auth J], W [auth D], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain N [auth A] Focus chain NA [auth I] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain N [auth A] Focus chain NA [auth I] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain W [auth D] Focus chain Z [auth E]
4Y8 Query on 4Y8 Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth I] SDF format, chain O [auth B] SDF format, chain OA [auth J] SDF format, chain R [auth C] SDF format, chain X [auth E] SDF format, chain U [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth I] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth J] MOL2 format, chain R [auth C] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth I] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth J] mmCIF format, chain R [auth C] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D]	AA [auth F] EA [auth G] HA [auth H] K [auth A] KA [auth I] AA [auth F], EA [auth G], HA [auth H], K [auth A], KA [auth I], O [auth B], OA [auth J], R [auth C], U [auth D], X [auth E]	1-hydroxypropan-2-one C₃ H₆ O₂ XLSMFKSTNGKWQX-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain K [auth A] Focus chain KA [auth I] Focus chain O [auth B] Focus chain OA [auth J] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain K [auth A] Focus chain KA [auth I] Focus chain O [auth B] Focus chain OA [auth J] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain T [auth C] SDF format, chain MA [auth I] SDF format, chain CA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain T [auth C] MOL2 format, chain MA [auth I] MOL2 format, chain CA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain T [auth C] mmCIF format, chain MA [auth I] mmCIF format, chain CA [auth F]	CA [auth F], M [auth A], MA [auth I], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth F] Focus chain M [auth A] Focus chain MA [auth I] Focus chain T [auth C] Interactions & Density Focus chain CA [auth F] Focus chain M [auth A] Focus chain MA [auth I] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.232 (Depositor), 0.232 (DCC)
R-Value Work: 0.191 (Depositor), 0.192 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.085	α = 90
b = 103.085	β = 90
c = 492.895	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-06-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-06-12
Type: Initial release
Version 1.1: 2020-07-22
Changes: Database references
Version 1.2: 2024-10-23
Changes: Advisory, Data collection, Database references, Structure summary