1YE6 | pdb_00001ye6

Crystal structure of the Lys-274 to Arg mutant of Candida tenuis xylose reductase (AKR2B5) bound to NADP+

PDB DOI: https://doi.org/10.2210/pdb1YE6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Yamadazyma tenuis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2004-12-28 Released: 2005-02-01
Deposition Author(s): Leitgeb, S., Petschacher, B., Wilson, D.K., Nidetzky, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.192 (Depositor), 0.193 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Fine tuning of coenzyme specificity in family 2 aldo-keto reductases revealed by crystal structures of the Lys-274-->Arg mutant of Candida tenuis xylose reductase (AKR2B5) bound to NAD(+) and NADP(+).

Leitgeb, S., Petschacher, B., Wilson, D.K., Nidetzky, B.

(2005) FEBS Lett 579: 763-767

PubMed: 15670843 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2004.12.063
Primary Citation Related Structures:
1YE4, 1YE6

PubMed Abstract:
Aldo-keto reductases of family 2 employ single site replacement Lys-->Arg to switch their cosubstrate preference from NADPH to NADH. X-ray crystal structures of Lys-274-->Arg mutant of Candida tenuis xylose reductase (AKR2B5) bound to NAD+ and NADP+ were determined at a resolution of 2.4 and 2.3A, respectively. Due to steric conflicts in the NADP+-bound form, the arginine side chain must rotate away from the position of the original lysine side chain, thereby disrupting a network of direct and water-mediated interactions between Glu-227, Lys-274 and the cofactor 2'-phosphate and 3'-hydroxy groups. Because anchoring contacts of its Glu-227 are lost, the coenzyme-enfolding loop that becomes ordered upon binding of NAD(P)+ in the wild-type remains partly disordered in the NADP+-bound mutant. The results delineate a catalytic reaction profile for the mutant in comparison to wild-type.

Organizational Affiliation

Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/I, A-8010 Graz, Austria.

Macromolecule Content

Total Structure Weight: 147.94 kDa
Atom Count: 11,116
Modeled Residue Count: 1,276
Deposited Residue Count: 1,288
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-dependent D-xylose reductase	A, B, C, D	322	Yamadazyma tenuis	Mutation(s): 1 Gene Names: XYL1, XYLR EC: 1.1.1 (PDB Primary Data), 1.1.1.307 (UniProt)
UniProt
Find proteins for O74237 (Candida tenuis) Explore O74237 Go to UniProtKB: O74237
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O74237
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C]	F [auth A], L [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth C]
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth D] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D]	J [auth B], P [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain J [auth B] Focus chain P [auth D] Interactions & Density Focus chain J [auth B] Focus chain P [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	E [auth A] G [auth B] H [auth B] I [auth B] K [auth C] E [auth A], G [auth B], H [auth B], I [auth B], K [auth C], M [auth D], N [auth D], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D]