4DEV | pdb_00004dev

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

PDB DOI: https://doi.org/10.2210/pdb4DEV/pdb

Classification: HYDROLASE
Organism(s): Butyrivibrio proteoclasticus B316
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-01-22 Released: 2013-02-13
Deposition Author(s): Till, M., Arcus, V.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.224 (Depositor), 0.224 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (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: 371.7 kDa
Atom Count: 25,485
Modeled Residue Count: 2,980
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): 1 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain LA [auth H] SDF format, chain T [auth D] SDF format, chain Z [auth E] SDF format, chain K [auth A] SDF format, chain AA [auth E] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain T [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth E] mmCIF format, chain GA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain T [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth E]	AA [auth E] GA [auth G] HA [auth G] K [auth A] LA [auth H] AA [auth E], GA [auth G], HA [auth G], K [auth A], LA [auth H], T [auth D], Z [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain T [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain T [auth D] Focus chain Z [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain IA [auth G] SDF format, chain Q [auth C] MOL2 format, chain IA [auth G] MOL2 format, chain Q [auth C] mmCIF format, chain IA [auth G] mmCIF format, chain Q [auth C]	IA [auth G], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IA [auth G] Focus chain Q [auth C] Interactions & Density Focus chain IA [auth G] Focus chain Q [auth C]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain JA [auth H] SDF format, chain KA [auth H] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain V [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain DA [auth F] SDF format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain V [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth F] MOL2 format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain V [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain BA [auth F]	BA [auth F] CA [auth F] DA [auth F] EA [auth G] FA [auth G] BA [auth F], CA [auth F], DA [auth F], EA [auth G], FA [auth G], I [auth A], J [auth A], JA [auth H], KA [auth H], M [auth B], N [auth B], O [auth C], P [auth C], R [auth D], S [auth D], U [auth D], V [auth D], W [auth E], X [auth E], Y [auth E]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224 (Depositor), 0.224 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.112	α = 89.96
b = 95.786	β = 99.74
c = 98.787	γ = 92.5

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Till, M.

Arcus, V.L.

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