Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.87 kDa 
• Atom Count: 1443 
• Residue Count: 167 
• Unique protein chains: 1

2PKP

Crystal structure of 3-isopropylmalate dehydratase (leuD)from Methhanocaldococcus Jannaschii DSM2661 (MJ1271)

• DOI: 10.2210/pdb2PKP/pdb

• Classification: LYASE
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-18 Released: 2008-04-22 
• Deposition Author(s): Jeyakanthan, J., Gayathri, D.R., Velmurugan, D., Agari, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 

Literature

Substrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of the small subunit

Jeyakanthan, J., Drevland, R.M., Gayathri, D.R., Velmurugan, D., Shinkai, A., Kuramitsu, S., Yokoyama, S., Graham, D.E.

(2010) Biochemistry 49: 2687-2696

• PubMed: 20170198 
• DOI: 10.1021/bi901766z
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The aconitase family of hydro-lyase enzymes includes three classes of proteins that catalyze the isomerization of alpha-hydroxy acids to beta-hydroxy acids. Besides aconitase, isopropylmalate isomerase (IPMI) proteins specifically catalyze the isomerization of alpha,beta-dicarboxylates with hydrophobic gamma-chain groups, and homoaconitase (HACN) proteins catalyze the isomerization of tricarboxylates with variable chain length gamma-carboxylate groups. These enzymes' stereospecific hydro-lyase activities make them attractive catalysts to produce diastereomers from unsaturated precursors. However, sequence similarity and convergent evolution among these proteins lead to widespread misannotation and uncertainty about gene function. To find the substrate specificity determinants of homologous IPMI and HACN proteins from Methanocaldococcus jannaschii, the small-subunit HACN protein (MJ1271) was crystallized for X-ray diffraction. The structural model showed characteristic residues in a flexible loop region between alpha2 and alpha3 that distinguish HACN from IPMI and aconitase proteins. Site-directed mutagenesis of MJ1271 produced loop-region variant proteins that were reconstituted with wild-type MJ1003 large-subunit protein. The heteromers formed promiscuous hydro-lyases with reduced activity but broader substrate specificity. Both R26K and R26V variants formed relatively efficient IPMI enzymes, while the T27A variant had uniformly lower specificity constants for both IPMI and HACN substrates. The R26V T27Y variant resembles the MJ1277 IPMI small subunit in its flexible loop sequence but demonstrated the broad substrate specificity of the R26V variant. These mutations may reverse the evolution of HACN activity from an ancestral IPMI gene, demonstrating the evolutionary potential for promiscuity in hydro-lyase enzymes. Understanding these specificity determinants enables the functional reannotation of paralogous HACN and IPMI genes in numerous genome sequences. These structural and kinetic results will help to engineer new stereospecific hydro-lyase enzymes for chemoenzymatic syntheses.

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Organizational Affiliation: 

Life Science Group, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinch 30076, Taiwan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Homoaconitase small subunit	A	170	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: aksE, hacB, MJ1271 EC: 4.2.1.114
Find proteins for Q58667 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Go to UniProtKB:  Q58667

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.992	α = 90
b = 108.283	β = 90
c = 45.449	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-18 
• Released Date: 2008-04-22 
Deposition Author(s): Jeyakanthan, J., Gayathri, D.R., Velmurugan, D., Agari, Y., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance