› 4v7n

X-ray diffraction
2.3Å resolution

Glycocyamine kinase, beta-beta homodimer from marine worm Namalycastis sp., with transition state analog Mg(II)-ADP-NO3-glycocyamine.

Released:
DOI: 10.2210/pdb4v7n/pdb
PDB entry 4v7n coloured by chain, front view.
PDB entry 4v7n coloured by chain, side view.
PDB entry 4v7n coloured by chain, top view.
Source organism: Namalycastis sp. ST01
Primary publication:
Structural basis for the mechanism and substrate specificity of glycocyamine kinase, a phosphagen kinase family member.
Lim K, Pullalarevu S, Surabian KT, Howard A, Suzuki T, Moult J, Herzberg O
Biochemistry 49 2031-41 (2010)
PMID: 20121101

Function and Biology Details

Reaction catalysed: 
ATP + guanidinoacetate = ADP + phosphoguanidinoacetate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179403 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycocyamine kinase beta chain Chains: AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, BO, BP, BQ, BR
Molecule details ›
Chains: AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, BO, BP, BQ, BR
Length: 390 amino acids
Theoretical weight: 44.11 KDa
Source organism: Namalycastis sp. ST01
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AW42 (Residues: 1-390; Coverage: 100%)
Gene name: GK-beta
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand NMG 36 x NMG
Ligand ADP 36 x ADP
Ligand MG 36 x MG
Ligand NO3 36 x NO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 243.11Å b: 114.27Å c: 259.9Å
α: 90° β: 90.25° γ: 90°
R-values:
R R work R free
0.197 0.197 0.263
Expression system: Escherichia coli

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Citations

3 review citations

Tackling guanidinoacetic acid for advanced cellular bioenergetics.
Ostojic SM. (2017)
2 more