› 8xud

X-ray diffraction
3.49Å resolution

Crystal structure of adaptor NlpI in complex with endopeptidase MepS and PDZ-protease Prc

Released:
DOI: 10.2210/pdb8xud/pdb
PDB entry 8xud coloured by chain, front view.
PDB entry 8xud coloured by chain, side view.
PDB entry 8xud coloured by chain, top view.
Source organism: Escherichia coli K-12
Entry authors: Tzeng SR, Wang S, Huang CH

Function and Biology Details

Reactions catalysed: 
The enzyme shows specific recognition of a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr, and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. A typical cleavage is -Ala-Ala-|-Arg-Ala-Ala-Lys-Glu-Asn-Tyr-Ala-Leu-Ala-Ala.
GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + H(2)O = GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-alanine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-245059 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Lipoprotein NlpI Chains: A, B
Molecule details ›
Chains: A, B
Length: 297 amino acids
Theoretical weight: 34.08 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AFB1 (Residues: 20-294; Coverage: 100%)
Gene names: JW3132, b3163, nlpI, yhbM
Tail-specific protease Chains: C, D
Molecule details ›
Chains: C, D
Length: 688 amino acids
Theoretical weight: 77.52 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P23865 (Residues: 1-682; Coverage: 100%)
Gene names: JW1819, b1830, prc, tsp
Sequence domains:
Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 168 amino acids
Theoretical weight: 19.15 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AFV4 (Residues: 28-188; Coverage: 99%)
Gene names: JW2163, b2175, mepS, spr, yeiV
Sequence domains: NlpC/P60 family
Substrate peptide Chain: M
Molecule details ›
Chain: M
Length: 8 amino acids
Theoretical weight: 699 Da
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
Substrate peptide Chain: N
Molecule details ›
Chain: N
Length: 9 amino acids
Theoretical weight: 784 Da
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

1 bound ligand:
Ligand PO4 14 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE TPS 05A
Spacegroup: P43212
Unit cell:
a: 230.41Å b: 230.41Å c: 182.905Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.235 0.272
Expression system: Escherichia coli BL21(DE3)

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