› 2h5d

X-ray diffraction
0.9Å resolution

0.9A resolution crystal structure of alpha-lytic protease complexed with a transition state analogue, MeOSuc-Ala-Ala-Pro-Val boronic acid

Released:
DOI: 10.2210/pdb2h5d/pdb
PDB entry 2h5d coloured by chain, front view.
PDB entry 2h5d coloured by chain, side view.
PDB entry 2h5d coloured by chain, top view.
Source organism: Lysobacter enzymogenes
Primary publication:
Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis.
Fuhrmann CN, Daugherty MD, Agard DA
J Am Chem Soc 128 9086-102 (2006)
PMID: 16834383

Function and Biology Details

Reaction catalysed: 
Preferential cleavage: Ala-|-, Val-|- in bacterial cell walls, elastin and other proteins.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133512 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Alpha-lytic protease Chain: A
Molecule details ›
Chain: A
Length: 198 amino acids
Theoretical weight: 19.88 KDa
Source organism: Lysobacter enzymogenes
UniProt:
  • Canonical: P00778 (Residues: 200-397; Coverage: 53%)
Gene name: alpha-LP
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
MEOSUC-ALA-ALA-PRO-ALA BORONIC ACID INHIBITOR Chain: B
Molecule details ›
Chain: B
Length: 5 amino acids
Theoretical weight: 470 Da
Source organism: Lysobacter enzymogenes
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 8 x SO4
Ligand GOL 1 x GOL
1 modified residue:
Ligand B2V 1 x B2V

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P3221
Unit cell:
a: 65.768Å b: 65.768Å c: 79.554Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.081 not available 0.091
Expression system: Not provided

Quick links

Citations

10 review citations

Biochemistry and theory of proton-coupled electron transfer.
Migliore et al. (2014)
9 more

3 mentions without citation

Low barrier hydrogen bonds in protein structure and function.
Kemp et al. (2021)
2 more