2YEP | pdb_00002yep

STRUCTURE OF AN N-TERMINAL NUCLEOPHILE (NTN) HYDROLASE, OAT2, IN COMPLEX WITH GLUTAMATE

PDB DOI: https://doi.org/10.2210/pdb2YEP/pdb
Entry: 2YEP supersedes: 2W4N

Classification: TRANSFERASE
Organism(s): Streptomyces clavuligerus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-03-29 Released: 2011-09-07
Deposition Author(s): Chowdhury, R., Iqbal, A., Clifton, I.J., Schofield, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.236 (Depositor), 0.256 (DCC)
R-Value Work:
0.218 (Depositor), 0.214 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 3.2 of the entry. See complete history.

Literature

Structural and Biochemical Analyses Reveal How Ornithine Acetyl Transferase Binds Acidic and Basic Amino Acid Substrates.

Iqbal, A., Clifton, I.J., Chowdhury, R., Ivison, D., Domene, C., Schofield, C.J.

(2011) Org Biomol Chem 9: 6219

PubMed: 21796301 Search on PubMed
DOI: https://doi.org/10.1039/c1ob05554b
Primary Citation Related Structures:
2YEP

PubMed Abstract:
Structural and biochemical analyses reveal how ornithine acetyl-transferases catalyse the reversible transfer of an acetyl-group from a basic (ornithine) to an acidic (glutamate) amino acid by employing a common mechanism involving an acetyl-enzyme intermediate but using different side chain binding modes.

Organizational Affiliation

Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.

Macromolecule Content

Total Structure Weight: 167.23 kDa
Atom Count: 11,651
Modeled Residue Count: 1,507
Deposited Residue Count: 1,572
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN	A, C, E, G	180	Streptomyces clavuligerus	Mutation(s): 0 EC: 2.3.1.35
UniProt
Find proteins for P0DJQ5 (Streptomyces clavuligerus) Explore P0DJQ5 Go to UniProtKB: P0DJQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DJQ5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN	B, D, H	213	Streptomyces clavuligerus	Mutation(s): 0 EC: 2.3.1.35
UniProt
Find proteins for P0DJQ5 (Streptomyces clavuligerus) Explore P0DJQ5 Go to UniProtKB: P0DJQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DJQ5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN	F	213	Streptomyces clavuligerus	Mutation(s): 0 EC: 2.3.1.35
UniProt
Find proteins for P0DJQ5 (Streptomyces clavuligerus) Explore P0DJQ5 Go to UniProtKB: P0DJQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DJQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLU Query on GLU Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B]	I [auth B], J [auth C]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain I [auth B] Focus chain J [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth G] SDF format, chain K [auth E] MOL2 format, chain L [auth G] MOL2 format, chain K [auth E] mmCIF format, chain L [auth G] mmCIF format, chain K [auth E]	K [auth E], L [auth G]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth E] Focus chain L [auth G] Interactions & Density Focus chain K [auth E] Focus chain L [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TH5 Query on TH5	B, D, H	L-PEPTIDE LINKING	C₆ H₁₁ N O₄		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.236 (Depositor), 0.256 (DCC)
R-Value Work: 0.218 (Depositor), 0.214 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.22	α = 90
b = 73.424	β = 93.26
c = 172.327	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-09-07

Deposition Author(s):

This entry supersedes: 2W4N

Revision History (Full details and data files)

Version 1.0: 2011-09-07
Type: Initial release
Version 1.1: 2017-09-13
Changes: Data collection
Version 2.0: 2019-05-15
Changes: Data collection, Derived calculations, Experimental preparation, Polymer sequence
Version 3.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other
Version 3.1: 2023-12-20
Changes: Refinement description
Version 3.2: 2024-11-13
Changes: Structure summary