PDBsum entry 4x8o

Transferase

PDB id: 4x8o

Contents

Protein chains

214 a.a.

Ligands

AP5 ×2

Metals

_NA

_MG ×2

Waters ×337

PDB id:

4x8o

Name:

Transferase

Title:

Crystal structure of e. Coli adenylate kinase y171w mutant in complex with inhibitor ap5a

Structure:

Adenylate kinase. Chain: a, b. Synonym: ak,atp-amp transphosphorylase,atp:amp phosphotransferase, adenylate monophosphate kinase. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: adk, dnaw, plsa, b0474, jw0463. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.180 R-free: 0.240

Authors:

A.E.Sauer-Eriksson,M.Kovermann,J.Aden,C.Grundstrom,M.Wolf-Watz, U.H.Sauer

Key ref:

M.Kovermann et al. (2015). Structural basis for catalytically restrictive dynamics of a high-energy enzyme state. Nat Commun, 6, 7644. PubMed id: 26138143 DOI: 10.1038/ncomms8644

Date:

10-Dec-14 Release date: 15-Jul-15

Protein chains

P69441  (KAD_ECOLI) -  Adenylate kinase from Escherichia coli (strain K12)

Seq: 214 a.a.

Struc: 214 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.7.4.3 - adenylate kinase.
• Reaction: AMP + ATP = 2 ADP

AMP + ATP (Bound ligand (Het Group name = AP5) matches with 54.39% similarity) = 2 × ADP

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

reference

DOI no: 10.1038/ncomms8644

Nat Commun 6:7644 (2015)

PubMed id: 26138143

Structural basis for catalytically restrictive dynamics of a high-energy enzyme state.

M.Kovermann, J.Ådén, C.Grundström, A.E.Sauer-Eriksson, U.H.Sauer, M.Wolf-Watz.

ABSTRACT

An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or 'invisible' states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme's catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes' conformational dynamics and hence their catalytic power-a key aspect in rational design of enzymes catalysing novel reactions.