5HOE | pdb_00005hoe

Crystal structrue of Est24, a carbohydrate acetylesterase from Sinorhizobium meliloti

PDB DOI: https://doi.org/10.2210/pdb5HOE/pdb

Classification: HYDROLASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-01-19 Released: 2016-04-27
Deposition Author(s): Oh, C., Ryu, B.H., An, D.R., Nguyen, D.D., Yoo, W., Kim, T., Ngo, D.T., Kim, H.S., Park, J.S., Kim, K.K., Kim, T.D.
Funding Organization(s): Korea Government, Rural Development Administration, National Research Foundation of Korea

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.216 (Depositor), 0.218 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural and Biochemical Characterization of an Octameric Carbohydrate Acetylesterase from Sinorhizobium meliloti.

Oh, C., Ryu, B.H., An, D.R., Nguyen, D.D., Yoo, W., Kim, T., Ngo, T.D., Kim, H.S., Kim, K.K., Kim, T.D.

(2016) FEBS Lett 590: 1242-1252

PubMed: 26991446 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12135
Primary Citation Related Structures:
5HOE

PubMed Abstract:
Carbohydrate acetylesterases, which have a highly specific role among plant-interacting bacterial species, remove the acetyl groups from plant carbohydrates. Here, we determined the crystal structure of Est24, an octameric carbohydrate acetylesterase from Sinorhizobium meliloti, at 1.45 Å resolution and investigated its biochemical properties. The structure of Est24 consisted of five parallel β strands flanked by α helices, which formed an octameric assembly with two distinct interfaces. The deacetylation activity of Est24 and its mutants around the substrate-binding pocket was investigated using several substrates, including glucose pentaacetate and acetyl alginate. Elucidation of the structure-function relationships of Est24 could provide valuable opportunities for biotechnological explorations.

Organizational Affiliation

Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea.

Macromolecule Content

Total Structure Weight: 100.94 kDa
Atom Count: 7,606
Modeled Residue Count: 860
Deposited Residue Count: 920
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase	A, B, C, D	230	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: SMa1993
UniProt
Find proteins for Q92XZ6 (Rhizobium meliloti (strain 1021)) Explore Q92XZ6 Go to UniProtKB: Q92XZ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92XZ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain G [auth B] MOL2 format, chain J [auth D] MOL2 format, chain G [auth B] mmCIF format, chain J [auth D] mmCIF format, chain G [auth B]	G [auth B], J [auth D]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], H [auth C], I [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.216 (Depositor), 0.218 (DCC)
R-Value Work: 0.172 (Depositor), 0.173 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.089	α = 90
b = 88.626	β = 114.3
c = 86.148	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-04-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Korea Government	Korea, Republic Of	2012R1A1A2000910
Rural Development Administration	Korea, Republic Of	SSAC PJ008107
National Research Foundation of Korea	Korea, Republic Of	2011-0028878

Revision History (Full details and data files)

Version 1.0: 2016-04-27
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description