3Q6J

Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M Oxidoreductase/Carboxylase

• PDB DOI: https://doi.org/10.2210/pdb3Q6J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Xanthobacter autotrophicus Py2
• Mutation(s): No 


• Deposited: 2011-01-01 Released: 2011-02-16 
• Deposition Author(s): Pandey, A.S., Mulder, D.W., Ensign, S.A., Peters, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.221 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M oxidoreductase/carboxylase.

Pandey, A.S., Mulder, D.W., Ensign, S.A., Peters, J.W.

(2011) FEBS Lett 585: 459-464

• PubMed: 21192936 
• DOI: https://doi.org/10.1016/j.febslet.2010.12.035
• Primary Citation of Related Structures:  
  3Q6J


• PubMed Abstract: 
  

  The structure of 2-ketopropyl coenzyme M oxidoreductase/carboxylase (2-KPCC) has been determined in a state in which CO(2) is observed providing insights into the mechanism of carboxylation. In the substrate encapsulated state of the enzyme, CO(2) is bound at the base of a narrow hydrophobic substrate access channel. The base of the channel is demarcated by a transition from a hydrophobic to hydrophilic environment where CO(2) is located in position for attack on the carbanion of the ketopropyl group of the substrate to ultimately produce acetoacetate. This binding mode effectively discriminates against H(2)O and prevents protonation of the ketopropyl leaving group.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 118.5 kDa 
• Atom Count: 9,351 
• Modelled Residue Count: 1,044 
• Deposited Residue Count: 1,046 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxopropyl-CoM reductase, carboxylating	A, B	523	Xanthobacter autotrophicus Py2	Mutation(s): 0  EC: 1.8.1.5
UniProt
Find proteins for Q56839 (Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)) Explore Q56839  Go to UniProtKB:  Q56839

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], L [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP	C [auth A], K [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
KPC	E [auth A]	(2-[2-KETOPROPYLTHIO]ETHANESULFONATE C5 H10 O4 S2 CRNXHFXAXBWIRH-UHFFFAOYSA-N
COM	M [auth B]	1-THIOETHANESULFONIC ACID C2 H6 O3 S2 ZNEWHQLOPFWXOF-UHFFFAOYSA-N
BCT	G [auth A], J [auth B]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
ACN	I [auth B]	ACETONE C3 H6 O CSCPPACGZOOCGX-UHFFFAOYSA-N
CO2	H [auth A]	CARBON DIOXIDE C O2 CURLTUGMZLYLDI-UHFFFAOYSA-N
MG	F [auth A], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.221 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.466	α = 90
b = 59.803	β = 102.28
c = 105.463	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-16 
Deposition Author(s): Pandey, A.S., Mulder, D.W., Ensign, S.A., Peters, J.W.

Revision History  

• Version 1.0: 2011-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description