4D5E

Crystal Structure of recombinant wildtype CDH

PDB DOI: https://doi.org/10.2210/pdb4D5E/pdb

Classification: HYDROLASE
Organism(s): Azoarcus olearius
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-11-03 Released: 2015-01-21
Deposition Author(s): Loschonsky, S., Wacker, T., Waltzer, S., Giovannini, P.P., McLeish, M.J., Andrade, S.L.A., Mueller, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.147
R-Value Work: 0.122
R-Value Observed: 0.123

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Extended Reaction Scope of Thiamine Diphosphate Dependent Cyclohexane-1,2-Dione Hydrolase: From C-C Bond Cleavage to C-C Bond Ligation.

Loschonsky, S., Wacker, T., Waltzer, S., Giovannini, P.P., Mcleish, M.J., Andrade, S.L.A., Muller, M.

(2014) Angew Chem Int Ed Engl 53: 14402

PubMed: 25382418 Search on PubMed
DOI: https://doi.org/10.1002/anie.201408287
Primary Citation of Related Structures:
4D5E, 4D5G

PubMed Abstract:
ThDP-dependent cyclohexane-1,2-dione hydrolase (CDH) catalyzes the CC bond cleavage of cyclohexane-1,2-dione to 6-oxohexanoate, and the asymmetric benzoin condensation between benzaldehyde and pyruvate. One of the two reactivities of CDH was selectively knocked down by mutation experiments. CDH-H28A is much less able to catalyze the CC bond formation, while the ability for CC bond cleavage is still intact. The double variant CDH-H28A/N484A shows the opposite behavior and catalyzes the addition of pyruvate to cyclohexane-1,2-dione, resulting in the formation of a tertiary alcohol. Several acyloins of tertiary alcohols are formed with 54-94 % enantiomeric excess. In addition to pyruvate, methyl pyruvate and butane-2,3-dione are alternative donor substrates for CC bond formation. Thus, the very rare aldehyde-ketone cross-benzoin reaction has been solved by design of an enzyme variant.

Organizational Affiliation

Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104 Freiburg (Germany).

Macromolecule Content

Total Structure Weight: 133.6 kDa
Atom Count: 10,559
Modelled Residue Count: 1,173
Deposited Residue Count: 1,178
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOHEXANE-1,2-DIONE HYDROLASE	A, B	589	Azoarcus olearius	Mutation(s): 0 EC: 3.7.1.11
UniProt
Find proteins for P0CH62 (Azoarcus sp) Explore P0CH62 Go to UniProtKB: P0CH62
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CH62
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain P [auth B]	C [auth A], P [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain P [auth B]
TPP Query on TPP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain Q [auth B]	D [auth A], Q [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain Q [auth B]
2PE Query on 2PE Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain V [auth B] SDF format, chain X [auth B] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] MOL2 format, chain X [auth B] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B] mmCIF format, chain X [auth B]	M [auth A], V [auth B], X [auth B]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain V [auth B] Focus chain X [auth B] Interactions & Density Focus chain M [auth A] Focus chain V [auth B] Focus chain X [auth B]
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A]	H [auth A], J [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain J [auth A]
1PG Query on 1PG Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C₁₁ H₂₄ O₆ SLNYBUIEAMRFSZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain R [auth B]	E [auth A], R [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain R [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] K [auth A] N [auth A] AA [auth B], BA [auth B], CA [auth B], K [auth A], N [auth A], O [auth A], W [auth B], Y [auth B], Z [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain K [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain W [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain K [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain W [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth B] MOL2 format, chain F [auth A] MOL2 format, chain S [auth B] mmCIF format, chain F [auth A] mmCIF format, chain S [auth B]	F [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain S [auth B] Interactions & Density Focus chain F [auth A] Focus chain S [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain G [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain G [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	G [auth A], T [auth B], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain G [auth A] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.147
R-Value Work: 0.122
R-Value Observed: 0.123
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.188	α = 90
b = 123.188	β = 90
c = 143.07	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-01-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-01-21
Type: Initial release
Version 1.1: 2015-05-06
Changes: Database references
Version 1.2: 2017-08-23
Changes: Advisory, Data collection
Version 1.3: 2024-05-08
Changes: Advisory, Data collection, Database references, Derived calculations, Other