3U37 | pdb_00003u37

An Acetyl Xylan Esterase (Est2A) from the Rumen Bacterium Butyrivibrio proteoclasticus.

PDB DOI: https://doi.org/10.2210/pdb3U37/pdb

Classification: HYDROLASE
Organism(s): Butyrivibrio proteoclasticus B316
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-10-05 Released: 2013-02-13
Deposition Author(s): Till, M., Arcus, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.242 (Depositor), 0.248 (DCC)
R-Value Work:
0.206 (Depositor), 0.211 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure and function of an acetyl xylan esterase (Est2A) from the rumen bacterium Butyrivibrio proteoclasticus.

Till, M., Goldstone, D.C., Attwood, G.T., Moon, C.D., Kelly, W.J., Arcus, V.L.

(2013) Proteins 81: 911-917

PubMed: 23345031 Search on PubMed
DOI: https://doi.org/10.1002/prot.24254
Primary Citation Related Structures:
3U37, 4DEV

PubMed Abstract:
Butyrivibrio proteoclasticus is a significant component of the microbial population of the rumen of dairy cattle. It is a xylan-degrading organism whose genome encodes a large number of open reading frames annotated as fiber-degrading enzymes. We have determined the three-dimensional structure of Est2A, an acetyl xylan esterase from B. proteoclasticus, at 2.1 Å resolution, along with the structure of an inactive mutant (H351A) at 2.0 Å resolution. The structure reveals two domains-a C-terminal SGNH domain and an N-terminal jelly-roll domain typical of CE2 family structures. The structures are accompanied by experimentally determined enzymatic parameters against two model substrates, para-nitrophenyl acetate and para-nitrophenyl butyrate. The suite of fiber-degrading enzymes produced by B. proteoclasticus provides a rich source of new enzymes of potential use in industrial settings.

Organizational Affiliation

Department of Biological Sciences, University of Waikato, Hamilton, New Zealand.

Macromolecule Content

Total Structure Weight: 370.76 kDa
Atom Count: 24,861
Modeled Residue Count: 2,990
Deposited Residue Count: 3,264
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-xylan esterase Est2A	A, B, C, D, E A, B, C, D, E, F, G, H	408	Butyrivibrio proteoclasticus B316	Mutation(s): 0 Gene Names: est2A, bpr_I2939
UniProt
Find proteins for E0RVY7 (Butyrivibrio proteoclasticus (strain ATCC 51982 / DSM 14932 / B316)) Explore E0RVY7 Go to UniProtKB: E0RVY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E0RVY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain R [auth H] SDF format, chain Q [auth G] SDF format, chain P [auth F] SDF format, chain O [auth F] SDF format, chain N [auth E] SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain S [auth H] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth F] MOL2 format, chain O [auth F] MOL2 format, chain N [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain S [auth H] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth F] mmCIF format, chain O [auth F] mmCIF format, chain N [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] L [auth C] M [auth D] N [auth E] I [auth A], J [auth B], L [auth C], M [auth D], N [auth E], O [auth F], P [auth F], Q [auth G], R [auth H], S [auth H]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.242 (Depositor), 0.248 (DCC)
R-Value Work: 0.206 (Depositor), 0.211 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.128	α = 99.8
b = 90.282	β = 90.21
c = 99.175	γ = 92.56

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Till, M.

Arcus, V.

Revision History (Full details and data files)

Version 1.0: 2013-02-13
Type: Initial release
Version 1.1: 2013-04-17
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description