7CI0 | pdb_00007ci0

Microbial Hormone-sensitive lipase E53 mutant S162A

PDB DOI: https://doi.org/10.2210/pdb7CI0/pdb

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

Deposited: 2020-07-06 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: 1.70 Å
R-Value Free:
0.191 (Depositor), 0.192 (DCC)
R-Value Work:
0.171 (Depositor), 0.173 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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 PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fmicb.2021.798194
Primary Citation 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: 138.73 kDa
Atom Count: 10,881
Modeled Residue Count: 1,236
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A074MDU6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain JB [auth D] MOL2 format, chain JB [auth D] mmCIF format, chain JB [auth D]	JB [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain JB [auth D] Interactions & Density Focus chain JB [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain XA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain XA [auth C]	W [auth B], XA [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Focus chain XA [auth C] Interactions & Density Focus chain W [auth B] Focus chain XA [auth C]
NPO Query on NPO Download:Ideal Coordinates CCD File SDF format, chain DB [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain X [auth B] SDF format, chain Z [auth B] SDF format, chain OB [auth D] SDF format, chain EB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain EB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain OB [auth D] mmCIF format, chain EB [auth D]	DB [auth D] E [auth A] EB [auth D] F [auth A] G [auth A] DB [auth D], E [auth A], EB [auth D], F [auth A], G [auth A], NA [auth C], OA [auth C], OB [auth D], PA [auth C], X [auth B], Z [auth B]	P-NITROPHENOL C₆ H₅ N O₃ BTJIUGUIPKRLHP-UHFFFAOYSA-N		Interactions Focus chain DB [auth D] Focus chain E [auth A] Focus chain EB [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain OB [auth D] Focus chain PA [auth C] Focus chain X [auth B] Focus chain Z [auth B] Interactions & Density Focus chain DB [auth D] Focus chain E [auth A] Focus chain EB [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain OB [auth D] Focus chain PA [auth C] Focus chain X [auth B] Focus chain Z [auth B]
6NA Query on 6NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain P [auth A] SDF format, chain H [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain H [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain H [auth A]	AA [auth B], H [auth A], P [auth A]	HEXANOIC ACID C₆ H₁₂ O₂ FUZZWVXGSFPDMH-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain H [auth A] Focus chain P [auth A] Interactions & Density Focus chain AA [auth B] Focus chain H [auth A] Focus chain P [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain FB [auth D] SDF format, chain I [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain I [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain I [auth A]	FB [auth D], I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FB [auth D] Focus chain I [auth A] Interactions & Density Focus chain FB [auth D] Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain PB [auth D] SDF format, chain V [auth A] SDF format, chain KA [auth B] SDF format, chain CB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain PB [auth D] MOL2 format, chain V [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain CB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain PB [auth D] mmCIF format, chain V [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain CB [auth C]	CB [auth C], KA [auth B], LA [auth B], PB [auth D], V [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CB [auth C] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain PB [auth D] Focus chain V [auth A] Interactions & Density Focus chain CB [auth C] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain PB [auth D] Focus chain V [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain NB [auth D] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain YA [auth C] SDF format, chain WA [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain WA [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain NB [auth D] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain WA [auth C]	IA [auth B] NB [auth D] R [auth A] S [auth A] T [auth A] IA [auth B], NB [auth D], R [auth A], S [auth A], T [auth A], TA [auth C], U [auth A], WA [auth C], YA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain NB [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain WA [auth C] Focus chain YA [auth C] Interactions & Density Focus chain IA [auth B] Focus chain NB [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain WA [auth C] Focus chain YA [auth C]
DIO Query on DIO Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain JA [auth B] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain VA [auth C] SDF format, chain Q [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain Q [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain Q [auth A]	AB [auth C] JA [auth B] M [auth A] O [auth A] Q [auth A] AB [auth C], JA [auth B], M [auth A], O [auth A], Q [auth A], VA [auth C]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain JA [auth B] Focus chain M [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain VA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain JA [auth B] Focus chain M [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain VA [auth C]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain HB [auth D] SDF format, chain IB [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LB [auth D] SDF format, chain MB [auth D] SDF format, chain SA [auth C] SDF format, chain UA [auth C] SDF format, chain RA [auth C] SDF format, chain KB [auth D] SDF format, chain FA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain SA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain KB [auth D] MOL2 format, chain FA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain HB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain MB [auth D] mmCIF format, chain SA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain KB [auth D] mmCIF format, chain FA [auth B]	BA [auth B] BB [auth C] CA [auth B] FA [auth B] HB [auth D] BA [auth B], BB [auth C], CA [auth B], FA [auth B], HB [auth D], IB [auth D], K [auth A], KB [auth D], L [auth A], LB [auth D], MB [auth D], RA [auth C], SA [auth C], UA [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain FA [auth B] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain K [auth A] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain UA [auth C] Interactions & Density Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain FA [auth B] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain K [auth A] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain UA [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain HA [auth B] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain QA [auth C] SDF format, chain ZA [auth C] SDF format, chain Y [auth B] SDF format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain EA [auth B]	DA [auth B] EA [auth B] GA [auth B] GB [auth D] HA [auth B] DA [auth B], EA [auth B], GA [auth B], GB [auth D], HA [auth B], J [auth A], N [auth A], QA [auth C], Y [auth B], ZA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain J [auth A] Focus chain N [auth A] Focus chain QA [auth C] Focus chain Y [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain J [auth A] Focus chain N [auth A] Focus chain QA [auth C] Focus chain Y [auth B] Focus chain ZA [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain MA [auth B] MOL2 format, chain MA [auth B] mmCIF format, chain MA [auth B]	MA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain MA [auth B] Interactions & Density Focus chain MA [auth B]