2QF7

Crystal structure of a complete multifunctional pyruvate carboxylase from Rhizobium etli

PDB DOI: https://doi.org/10.2210/pdb2QF7/pdb

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

Deposited: 2007-06-27 Released: 2007-09-04
Deposition Author(s): St Maurice, M., Surinya, K.H., Rayment, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.223
R-Value Work: 0.178
R-Value Observed: 0.180

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Ligand Structure Quality Assessment

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

Literature

Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme

St Maurice, M., Reinhardt, L., Surinya, K.H., Attwood, P.V., Wallace, J.C., Cleland, W.W., Rayment, I.

(2007) Science 317: 1076-1079

PubMed: 17717183 Search on PubMed
DOI: https://doi.org/10.1126/science.1144504
Primary Citation of Related Structures:
2QF7

PubMed Abstract:
Biotin-dependent multifunctional enzymes carry out metabolically important carboxyl group transfer reactions and are potential targets for the treatment of obesity and type 2 diabetes. These enzymes use a tethered biotin cofactor to carry an activated carboxyl group between distantly spaced active sites. The mechanism of this transfer has remained poorly understood. Here we report the complete structure of pyruvate carboxylase at 2.0 angstroms resolution, which shows its domain arrangement. The structure, when combined with mutagenic analysis, shows that intermediate transfer occurs between active sites on separate polypeptide chains. In addition, domain rearrangements associated with activator binding decrease the distance between active-site pairs, providing a mechanism for allosteric activation. This description provides insight into the function of biotin-dependent enzymes and presents a new paradigm for multifunctional enzyme catalysis.

Organizational Affiliation

Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

Macromolecule Content

Total Structure Weight: 257.54 kDa
Atom Count: 17,618
Modelled Residue Count: 2,093
Deposited Residue Count: 2,330
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate carboxylase protein	A, B	1,165	Rhizobium etli CFN 42	Mutation(s): 1 Gene Names: pyc EC: 6.4.1.1
UniProt
Find proteins for Q2K340 (Rhizobium etli (strain CFN 42 / ATCC 51251)) Explore Q2K340 Go to UniProtKB: Q2K340
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2K340
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
AGS Query on AGS Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain J [auth A]	J [auth A], R [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B]	S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A]	E [auth A], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B]	K [auth A], T [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain T [auth B] Interactions & Density Focus chain K [auth A] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain H [auth A]	G [auth A], H [auth A], P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	C [auth A] D [auth A] F [auth A] M [auth B] N [auth B] C [auth A], D [auth A], F [auth A], M [auth B], N [auth B], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.223
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 234.729	α = 90
b = 93.258	β = 107.33
c = 137.222	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-09-04

Deposition Author(s):

St Maurice, M.

Surinya, K.H.

Rayment, I.

Revision History (Full details and data files)

Version 1.0: 2007-09-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.2: 2012-02-15
Changes: Non-polymer description

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Help and Resources

2QF7

Crystal structure of a complete multifunctional pyruvate carboxylase from Rhizobium etli

Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)