PDBsum entry 4rf8

Transferase

PDB id: 4rf8

Contents

Protein chains

686 a.a.

Ligands

ADP ×2

NO3 ×20

EPE ×2

Waters ×548

PDB id:

4rf8

Name:

Transferase

Title:

Crystal structure of double-domain arginine kinase from anthopleura japonicas in complex with adp

Structure:

Arginine kinase. Chain: a, b. Synonym: ak. Engineered: yes

Source:

Anthopleura japonica. Sea anemone. Organism_taxid: 67755. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.17Å R-factor: 0.195 R-free: 0.239

Authors:

Z.Wang,Z.Qiao,S.Ye,R.Zhang

Key ref:

Z.Wang et al. (2015). Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains. Acta Crystallogr D Biol Crystallogr, 71, 779-789. PubMed id: 25849389 DOI: 10.1107/S1399004715001169

Date:

25-Sep-14 Release date: 08-Apr-15

Protein chains

O15992  (KARG_ANTJA) -  Arginine kinase from Anthopleura japonica

Seq: 715 a.a.

Struc: 686 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.3.3 - arginine kinase.
• Reaction: L-arginine + ATP = N(omega)-phospho-L-arginine + ADP + H⁺

L-arginine + ATP = N(omega)-phospho-L-arginine (Bound ligand (Het Group name = ADP) corresponds exactly) + ADP + H(+)

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

reference

DOI no: 10.1107/S1399004715001169

Acta Crystallogr D Biol Crystallogr 71:779-789 (2015)

PubMed id: 25849389

Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.

Z.Wang, Z.Qiao, S.Ye, R.Zhang.

ABSTRACT

Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.