PDBsum entry 3dp9

Hydrolase

PDB id: 3dp9

Contents

Protein chains

229 a.a. *

Ligands

BIG ×2

Metals

IOD

Waters ×66

* Residue conservation analysis

PDB id:

3dp9

Name:

Hydrolase

Title:

Crystal structure of vibrio cholerae 5'-methylthioadenosine/s-adenosyl homocysteine nucleosidase (mtan) complexed with butylthio-dadme- immucillin a

Structure:

Mta/sah nucleosidase. Chain: a, c. Engineered: yes

Source:

Vibrio cholerae. Organism_taxid: 666. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.203 R-free: 0.264

Authors:

M.Ho,J.A.Gutierrez,T.Crowder,A.Rinaldo-Matthis,S.C.Almo,V.L.Schramm

Key ref:

J.A.Gutierrez et al. (2009). Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing. Nat Chem Biol, 5, 251-257. PubMed id: 19270684 DOI: 10.1038/nchembio.153

Date:

07-Jul-08 Release date: 10-Mar-09

Protein chains

Q9KPI8  (MTNN_VIBCH) -  5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

Seq: 231 a.a.

Struc: 229 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.2.9 - adenosylhomocysteine nucleosidase.
• Pathway: Autoinducer AI-2 Biosynthesis
• Reaction:
  1. S-adenosyl-L-homocysteine + H2O = S-(5-deoxy-D-ribos-5-yl)-L- homocysteine + adenine
  2. 5'-deoxyadenosine + H2O = 5-deoxy-D-ribose + adenine
  3. S-methyl-5'-thioadenosine + H2O = 5-(methylsulfanyl)-D-ribose + adenine

5'-deoxyadenosine (Bound ligand (Het Group name = BIG) matches with 41.38% similarity) + H2O = 5-deoxy-D-ribose + adenine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nchembio.153

Nat Chem Biol 5:251-257 (2009)

PubMed id: 19270684

Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing.

J.A.Gutierrez, T.Crowder, A.Rinaldo-Matthis, M.C.Ho, S.C.Almo, V.L.Schramm.

ABSTRACT

5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is a bacterial enzyme involved in S-adenosylmethionine-related quorum sensing pathways that induce bacterial pathogenesis factors. Transition state analogs MT-DADMe-Immucillin-A, EtT-DADMe-Immucillin-A and BuT-DADMe-Immucillin-A are slow-onset, tight-binding inhibitors of Vibrio cholerae MTAN (VcMTAN), with equilibrium dissociation constants of 73, 70 and 208 pM, respectively. Structural analysis of VcMTAN with BuT-DADMe-Immucillin-A revealed interactions contributing to the high affinity. We found that in V. cholerae cells, these compounds are potent MTAN inhibitors with IC(50) values of 27, 31 and 6 nM for MT-, EtT- and BuT-DADMe-Immucillin-A, respectively; the compounds disrupt autoinducer production in a dose-dependent manner without affecting growth. MT- and BuT-DADMe-Immucillin-A also inhibited autoinducer-2 production in enterohemorrhagic Escherichia coli O157:H7 with IC(50) values of 600 and 125 nM, respectively. BuT-DADMe-Immucillin-A inhibition of autoinducer-2 production in both strains persisted for several generations and caused reduction in biofilm formation. These results support MTAN's role in quorum sensing and its potential as a target for bacterial anti-infective drug design.

Selected figure(s)

Figure 2.
(a) Top, a dissociative transition state for E. coli with ribooxacarbenium ion character^10. Bottom, structures of stable analogs for an early dissociative transition state (ImmA) and a late dissociative transition state (DADMe-ImmA) depict differences in bond distances between the adenine leaving group and the ribosyl group, as well as charge localization. TS, transition state. (b) The structure of S-substituted DADMe-ImmA, along with MT, EtT and BuT substituents.

Figure 3.
(a) Overall structure of VcMTAN showing the asymmetric unit content with the inhibitor BuT-DADMe-ImmA bound in the active sites. (b) The active site of VcMTAN with a 2F[o] - F[c] map contoured at 1.2 surrounding the BuT-DADMe-ImmA inhibitor and the proposed nucleophilic water molecule. (c) Space-filling picture of the active site of VcMTAN with BuT-DADMe-ImmA in the active site. Grey represents hydrophobic regions of the protein, which interact with hydrophobic parts of the inhibitor. The red color shows parts of the protein that contain charged residues interacting with polar groups of the inhibitor, and green represents loop regions. (d) Schematic drawing of the BuT-DADMe-ImmA inhibitor bound in the active site of VcMTAN showing catalytic contacts.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Chem Biol (2009, 5, 251-257) copyright 2009.

Figures were selected by an automated process.