3WG6

Crystal structure of conjugated polyketone reductase C1 from Candida parapsilosis complexed with NADPH

PDB DOI: https://doi.org/10.2210/pdb3WG6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candida parapsilosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-07-28 Released: 2013-08-21
Deposition Author(s): Qin, H.-M., Yamamura, A., Miyakawa, T., Maruoka, S., Ohtsuka, J., Nagata, K., Kataoka, M., Shimizu, S., Tanokura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.242
R-Value Work: 0.182
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of conjugated polyketone reductase (CPR-C1) from Candida parapsilosis IFO 0708 complexed with NADPH.

Qin, H.M., Yamamura, A., Miyakawa, T., Kataoka, M., Maruoka, S., Ohtsuka, J., Nagata, K., Shimizu, S., Tanokura, M.

(2013) Proteins 81: 2059-2063

PubMed: 23852710 Search on PubMed
DOI: https://doi.org/10.1002/prot.24363
Primary Citation of Related Structures:
3WG6

PubMed Abstract:
Conjugated polyketone reductase (CPR-C1) from Candida parapsilosis IFO 0708 is a member of the aldo-keto reductase (AKR) superfamily and reduces ketopantoyl lactone to d-pantoyl lactone in a NADPH-dependent and stereospecific manner. We determined the crystal structure of CPR-C1.NADPH complex at 2.20 Å resolution. CPR-C1 adopted a triose-phosphate isomerase (TIM) barrel fold at the core of the structure in which Thr25 and Lys26 of the GXGTX motif bind uniquely to the adenosine 2'-phosphate group of NADPH. This finding provides a novel structural basis for NADPH binding of the AKR superfamily.

Organizational Affiliation

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.

Macromolecule Content

Total Structure Weight: 142.27 kDa
Atom Count: 10,104
Modelled Residue Count: 1,190
Deposited Residue Count: 1,228
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conjugated polyketone reductase C1	A, B, C, D	307	Candida parapsilosis	Mutation(s): 0 Gene Names: cpr-c1 EC: 1.1.1.358 (UniProt), 1.1.1 (UniProt)
UniProt
Find proteins for Q76L37 (Candida parapsilosis) Explore Q76L37 Go to UniProtKB: Q76L37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q76L37
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]