3TW6 | pdb_00003tw6

Structure of Rhizobium etli pyruvate carboxylase T882A with the allosteric activator, acetyl coenzyme-A

• PDB DOI: https://doi.org/10.2210/pdb3TW6/pdb

• Classification: LIGASE/ACTIVATOR
• Organism(s): Rhizobium etli CFN 42
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-09-21 Released: 2011-10-19 
• Deposition Author(s): St Maurice, M., Kumar, S., Lietzan, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Interaction between the biotin carboxyl carrier domain and the biotin carboxylase domain in pyruvate carboxylase from Rhizobium etli.

Lietzan, A.D., Menefee, A.L., Zeczycki, T.N., Kumar, S., Attwood, P.V., Wallace, J.C., Cleland, W.W., St Maurice, M.

(2011) Biochemistry 50: 9708-9723

• PubMed: 21958016 
• DOI: https://doi.org/10.1021/bi201277j
• Primary Citation Related Structures: 
  3TW6, 3TW7


• PubMed Abstract: 
  

  Pyruvate carboxylase (PC) catalyzes the ATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To effect catalysis, the tethered biotin of PC must gain access to active sites in both the biotin carboxylase domain and the carboxyl transferase domain. Previous studies have demonstrated that a mutation of threonine 882 to alanine in PC from Rhizobium etli renders the carboxyl transferase domain inactive and favors the positioning of biotin in the biotin carboxylase domain. We report the 2.4 Å resolution X-ray crystal structure of the Rhizobium etli PC T882A mutant which reveals the first high-resolution description of the domain interaction between the biotin carboxyl carrier protein domain and the biotin carboxylase domain. The overall quaternary arrangement of Rhizobium etli PC remains highly asymmetrical and is independent of the presence of allosteric activator. While biotin is observed in the biotin carboxylase domain, its access to the active site is precluded by the interaction between Arg353 and Glu248, revealing a mechanism for regulating carboxybiotin access to the BC domain active site. The binding location for the biotin carboxyl carrier protein domain demonstrates that tethered biotin cannot bind in the biotin carboxylase domain active site in the same orientation as free biotin, helping to explain the difference in catalysis observed between tethered biotin and free biotin substrates in biotin carboxylase enzymes. Electron density located in the biotin carboxylase domain active site is assigned to phosphonoacetate, offering a probable location for the putative carboxyphosphate intermediate formed during biotin carboxylation. The insights gained from the T882A Rhizobium etli PC crystal structure provide a new series of catalytic snapshots in PC and offer a revised perspective on catalysis in the biotin-dependent enzyme family.

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Organizational Affiliation: 
• Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 514.46 kDa 
• Atom Count: 32,812 
• Modeled Residue Count: 4,309 
• Deposited Residue Count: 4,660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate carboxylase protein	A, B, C, D	1,165	Rhizobium etli CFN 42	Mutation(s): 1  Gene Names: pyc, RHE_CH04002 EC: 6.4.1.1
UniProt
Find proteins for Q2K340 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2K340  Go to UniProtKB:  Q2K340

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	K [auth A], Y [auth C]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
ADP	BA [auth D], G [auth A], N [auth B], U [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BTI	Q [auth B]	5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL C10 H16 N2 O2 S ARDNWGMSCXSPBF-CIUDSAMLSA-N
PAE	X [auth C]	PHOSPHONOACETIC ACID C2 H5 O5 P XUYJLQHKOGNDPB-UHFFFAOYSA-N
ZN	CA [auth D], H [auth A], O [auth B], V [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	AA [auth D], E [auth A], F [auth A], L [auth B], M [auth B], S [auth C], T [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	DA [auth D], EA [auth D], I [auth A], J [auth A], P [auth B], R [auth B], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 370.445	α = 90
b = 91.55	β = 134.71
c = 261.354	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-19 
Deposition Author(s): St Maurice, M., Kumar, S., Lietzan, A.D.

Revision History  

• Version 1.0: 2011-10-19
  Type: Initial release
  
• Version 1.1: 2011-12-28
  Changes: Database references
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary