PDBsum entry 3ju6

Transferase

PDB id: 3ju6

Contents

Protein chains

361 a.a. *

Ligands

ARG

ANP

Waters ×1763

* Residue conservation analysis

PDB id:

3ju6

Name:

Transferase

Title:

Crystal structure of dimeric arginine kinase in complex with amppnp and arginine

Structure:

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

Source:

Apostichopus japonicus. Sea cucumber. Organism_taxid: 307972. Gene: ak. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.45Å R-factor: 0.214 R-free: 0.254

Authors:

X.Wu,S.Ye,S.Guo,W.Yan,M.Bartlam,Z.Rao

Key ref:

X.Wu et al. (2010). Structural basis for a reciprocating mechanism of negative cooperativity in dimeric phosphagen kinase activity. Faseb J, 24, 242-252. PubMed id: 19783784

Date:

14-Sep-09 Release date: 29-Sep-09

Protein chains

Q9XY07  (KARG_STIJA) -  Arginine kinase from Stichopus japonicus

Seq: 370 a.a.

Struc: 361 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 (Bound ligand (Het Group name = ARG) corresponds exactly) = N(omega)-phospho-L-arginine (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + ADP + H(+)

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

reference

Faseb J 24:242-252 (2010)

PubMed id: 19783784

Structural basis for a reciprocating mechanism of negative cooperativity in dimeric phosphagen kinase activity.

X.Wu, S.Ye, S.Guo, W.Yan, M.Bartlam, Z.Rao.

ABSTRACT

Phosphagen kinase (PK) family members catalyze the reversible phosphoryl transfer between phosphagen and ADP to reserve or release energy in cell energy metabolism. The structures of classic quaternary complexes of dimeric creatine kinase (CK) revealed asymmetric ligand binding states of two protomers, but the significance and mechanism remain unclear. To understand this negative cooperativity further, we determined the first structure of dimeric arginine kinase (dAK), another PK family member, at 1.75 A, as well as the structure of its ternary complex with AMPPNP and arginine. Further structural analysis shows that the ligand-free protomer in a ligand-bound dimer opens more widely than the protomers in a ligand-free dimer, which leads to three different states of a dAK protomer. The unexpected allostery of the ligand-free protomer in a ligand-bound dimer should be relayed from the ligand-binding-induced allostery of its adjacent protomer. Mutations that weaken the interprotomer connections dramatically reduced the catalytic activities of dAK, indicating the importance of the allosteric propagation mediated by the homodimer interface. These results suggest a reciprocating mechanism of dimeric PK, which is shared by other ATP related oligomeric enzymes, e.g., ATP synthase.