Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 220.75 kDa 
• Atom Count: 16984 
• Modelled Residue Count: 1941 
• Deposited Residue Count: 1976 
• Unique protein chains: 1

3CE6

Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with NAD and adenosine

• DOI: 10.2210/pdb3CE6/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-28 Released: 2008-09-16 
• Deposition Author(s): Reddy, M.C.M., Gokulan, K., Shetty, N.D., Owen, J.L., Ioerger, T.R., Sacchettini, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.238 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors.

Reddy, M.C., Kuppan, G., Shetty, N.D., Owen, J.L., Ioerger, T.R., Sacchettini, J.C.

(2008) Protein Sci 17: 2134-2144

• PubMed: 18815415 
• DOI: 10.1110/ps.038125.108
• Primary Citation of Related Structures:  
  3DHY, 2ZIZ, 2ZJ0, 2ZJ1, 3CE6


• PubMed Abstract: 
  

S-adenosylhomocysteine hydrolase (SAHH) is a ubiquitous enzyme that plays a central role in methylation-based processes by maintaining the intracellular balance between S-adenosylhomocysteine (SAH) and S-adenosylmethionine. We report the first prokaryotic crystal structure of SAHH, from Mycobacterium tuberculosis (Mtb), in complex with adenosine (ADO) and nicotinamide adenine dinucleotide. Structures of complexes with three inhibitors are also reported: 3'-keto aristeromycin (ARI), 2-fluoroadenosine, and 3-deazaadenosine. The ARI complex is the first reported structure of SAHH complexed with this inhibitor, and confirms the oxidation of the 3' hydroxyl to a planar keto group, consistent with its prediction as a mechanism-based inhibitor. We demonstrate the in vivo enzyme inhibition activity of the three inhibitors and also show that 2-fluoradenosine has bactericidal activity. While most of the residues lining the ADO-binding pocket are identical between Mtb and human SAHH, less is known about the binding mode of the homocysteine (HCY) appendage of the full substrate. We report the 2.0 A resolution structure of the complex of SAHH cocrystallized with SAH. The most striking change in the structure is that binding of HCY forces a rotation of His363 around the backbone to flip out of contact with the 5' hydroxyl of the ADO and opens access to a nearby channel that leads to the surface. This complex suggests that His363 acts as a switch that opens up to permit binding of substrate, then closes down after release of the cleaved HCY. Differences in the entrance to this access channel between human and Mtb SAHH are identified.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	494	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: ahcY, sahH, Rv3248c, MT3346, MTCY20B11.23c EC: 3.3.1.1
Find proteins for P9WGV3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGV3  Go to UniProtKB:  P9WGV3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	F [auth A], H [auth B], J [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ADN	E [auth A], G [auth B], I [auth C], K [auth D]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ADN	IC50:  500000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.238 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.04	α = 90
b = 112.133	β = 92.41
c = 100.234	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-28 
• Released Date: 2008-09-16 
Deposition Author(s): Reddy, M.C.M., Gokulan, K., Shetty, N.D., Owen, J.L., Ioerger, T.R., Sacchettini, J.C.

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance