2K1G | pdb_00002k1g

Solution NMR structure of lipoprotein spr from Escherichia coli K12. Northeast Structural Genomics target ER541-37-162


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 2K1G

This is version 1.2 of the entry. See complete history

Literature

Solution NMR structure of the NlpC/P60 domain of lipoprotein Spr from Escherichia coli: structural evidence for a novel cysteine peptidase catalytic triad.

Aramini, J.M.Rossi, P.Huang, Y.J.Zhao, L.Jiang, M.Maglaqui, M.Xiao, R.Locke, J.Nair, R.Rost, B.Acton, T.B.Inouye, M.Montelione, G.T.

(2008) Biochemistry 47: 9715-9717

  • DOI: https://doi.org/10.1021/bi8010779
  • Primary Citation Related Structures: 
    2K1G

  • PubMed Abstract: 

    Escherichia coli Spr is a membrane-anchored cell wall hydrolase. The solution NMR structure of the C-terminal NlpC/P60 domain of E. coli Spr described here reveals that the protein adopts a papain-like alpha+beta fold and identifies a substrate-binding cleft featuring several highly conserved residues. The active site features a novel Cys-His-His catalytic triad that appears to be a unique structural signature of this cysteine peptidase family. Moreover, the relative orientation of these catalytic residues is similar to that observed in the analogous Ser-His-His triad, a variant of the classic Ser-His-Asp charge relay system, suggesting the convergent evolution of a catalytic mechanism in quite distinct peptidase families.


  • Organizational Affiliation
    • Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA. jma@cabm.rutgers.edu

Macromolecule Content 

  • Total Structure Weight: 15.58 kDa 
  • Atom Count: 1,035 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 135 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipoprotein spr135Escherichia coli K-12Mutation(s): 0 
Gene Names: spryeiVb2175JW2163
EC: 3.4 (UniProt), 3.4.17.13 (UniProt)
UniProt
Find proteins for P0AFV4 (Escherichia coli (strain K12))
Explore P0AFV4 
Go to UniProtKB:  P0AFV4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFV4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references