7CIH

Microbial Hormone-sensitive lipase E53 mutant S285G

PDB DOI: https://doi.org/10.2210/pdb7CIH/pdb

Classification: HYDROLASE
Organism(s): Erythrobacter longus
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2020-07-07 Released: 2021-07-14
Deposition Author(s): Yang, X., Li, Z., Xu, X., Li, J.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.190
R-Value Work: 0.169

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanism and Structural Insights Into a Novel Esterase, E53, Isolated From Erythrobacter longus .

Ding, Y., Nie, L., Yang, X.C., Li, Y., Huo, Y.Y., Li, Z., Gao, Y., Cui, H.L., Li, J., Xu, X.W.

(2021) Front Microbiol 12: 798194-798194

PubMed: 35069500 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.3389/fmicb.2021.798194
Primary Citation of Related Structures:
7CI0, 7CIH, 7W8N

PubMed Abstract:
Esterases are a class of enzymes that split esters into an acid and an alcohol in a chemical reaction with water, having high potential in pharmaceutical, food and biofuel industrial applications. To advance the understanding of esterases, we have identified and characterized E53, an alkalophilic esterase from a marine bacterium Erythrobacter longus . The crystal structures of wild type E53 and three variants were solved successfully using the X-ray diffraction method. Phylogenetic analysis classified E53 as a member of the family IV esterase. The enzyme showed highest activity against p -nitrophenyl butyrate substrate at pH 8.5-9.5 and 40 ^°C. Based on the structural feature, the catalytic pocket was defined as R1 (catalytic center), R2 (pocket entrance), and R3 (end area of pocket) regions. Nine variants were generated spanning R1-R3 and thorough functional studies were performed. Detailed structural analysis and the results obtained from the mutagenesis study revealed that mutations in the R1 region could regulate the catalytic reaction in both positive and negative directions; expanding the bottleneck in R2 region has improved the enzymatic activity; and R3 region was associated with the determination of the pH pattern of E53. N166A in R3 region showed reduced activity only under alkaline conditions, and structural analysis indicated the role of N166 in stabilizing the loop by forming a hydrogen bond with L193 and G233. In summary, the systematic studies on E53 performed in this work provide structural and functional insights into alkaliphilic esterases and further our knowledge of these enzymes.

Organizational Affiliation

Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China.

Macromolecule Content

Total Structure Weight: 137.34 kDa
Atom Count: 10,685
Modelled Residue Count: 1,240
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B, C, D	314	Erythrobacter longus	Mutation(s): 1 Gene Names: EH31_02760
UniProt
Find proteins for A0A074MDU6 (Erythrobacter longus) Explore A0A074MDU6 Go to UniProtKB: A0A074MDU6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A074MDU6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D8F (Subject of Investigation/LOI) Query on D8F Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain JA [auth C] SDF format, chain S [auth B] SDF format, chain TA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth D]	E [auth A], JA [auth C], S [auth B], TA [auth D]	(4-nitrophenyl) hexanoate C₁₂ H₁₅ N O₄ OLRXUEYZKCCEKK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain JA [auth C] Focus chain S [auth B] Focus chain TA [auth D] Interactions & Density Focus chain E [auth A] Focus chain JA [auth C] Focus chain S [auth B] Focus chain TA [auth D]
NPO Query on NPO Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B]	DA [auth B], EA [auth B]	P-NITROPHENOL C₆ H₅ N O₃ BTJIUGUIPKRLHP-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EB [auth D] SDF format, chain HA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain HA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain HA [auth B]	EB [auth D], HA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EB [auth D] Focus chain HA [auth B] Interactions & Density Focus chain EB [auth D] Focus chain HA [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain R [auth B] SDF format, chain SA [auth C] SDF format, chain UA [auth D] SDF format, chain X [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain UA [auth D] MOL2 format, chain X [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain UA [auth D] mmCIF format, chain X [auth B]	G [auth A] I [auth A] KA [auth C] LA [auth C] MA [auth C] G [auth A], I [auth A], KA [auth C], LA [auth C], MA [auth C], NA [auth C], R [auth B], SA [auth C], UA [auth D], X [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain R [auth B] Focus chain SA [auth C] Focus chain UA [auth D] Focus chain X [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain R [auth B] Focus chain SA [auth C] Focus chain UA [auth D] Focus chain X [auth B]
DIO Query on DIO Download Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] mmCIF format, chain BB [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D]	BB [auth D], VA [auth D], W [auth B], WA [auth D]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Interactions & Density Focus chain BB [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain DB [auth D] SDF format, chain F [auth A] SDF format, chain GA [auth B] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain RA [auth C] SDF format, chain U [auth B] SDF format, chain XA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain XA [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain F [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain XA [auth D]	CA [auth B] CB [auth D] DB [auth D] F [auth A] GA [auth B] CA [auth B], CB [auth D], DB [auth D], F [auth A], GA [auth B], IA [auth C], J [auth A], K [auth A], P [auth A], Q [auth A], RA [auth C], U [auth B], XA [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain F [auth A] Focus chain GA [auth B] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth C] Focus chain U [auth B] Focus chain XA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain F [auth A] Focus chain GA [auth B] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth C] Focus chain U [auth B] Focus chain XA [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain FA [auth B] SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B] AB [auth D] BA [auth B] FA [auth B] H [auth A] AA [auth B], AB [auth D], BA [auth B], FA [auth B], H [auth A], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth C], PA [auth C], QA [auth C], T [auth B], V [auth B], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain FA [auth B] Focus chain H [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain T [auth B] Focus chain V [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain FA [auth B] Focus chain H [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain T [auth B] Focus chain V [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]