4D5E | pdb_00004d5e

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 (Depositor), 0.161 (DCC)
R-Value Work:
0.122 (Depositor), 0.138 (DCC)
R-Value Observed:
0.123 (Depositor)

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 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
Modeled Residue Count: 1,173
Deposited Residue Count: 1,178
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 P [auth B] SDF format, chain C [auth A] MOL2 format, chain P [auth B] MOL2 format, chain C [auth A] mmCIF format, chain P [auth B] mmCIF format, chain C [auth A]	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 Q [auth B] SDF format, chain D [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain D [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain D [auth A]	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 X [auth B] SDF format, chain V [auth B] SDF format, chain M [auth A] MOL2 format, chain X [auth B] MOL2 format, chain V [auth B] MOL2 format, chain M [auth A] mmCIF format, chain X [auth B] mmCIF format, chain V [auth B] mmCIF format, chain M [auth A]	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 J [auth A] SDF format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [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 R [auth B] SDF format, chain E [auth A] MOL2 format, chain R [auth B] MOL2 format, chain E [auth A] mmCIF format, chain R [auth B] mmCIF format, chain E [auth A]	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 Z [auth B] SDF format, chain Y [auth B] SDF format, chain W [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain K [auth A] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [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 S [auth B] SDF format, chain F [auth A] MOL2 format, chain S [auth B] MOL2 format, chain F [auth A] mmCIF format, chain S [auth B] mmCIF format, chain F [auth A]	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 U [auth B] SDF format, chain T [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain G [auth A]	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 (Depositor), 0.161 (DCC)
R-Value Work: 0.122 (Depositor), 0.138 (DCC)
R-Value Observed: 0.123 (Depositor)

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

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Ligand Structure Quality Assessment

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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