Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 50.10 kDa 
• Atom Count: 3858 
• Modelled Residue Count: 439 
• Deposited Residue Count: 440 
• Unique protein chains: 1

1A16

AMINOPEPTIDASE P FROM E. COLI WITH THE INHIBITOR PRO-LEU

• PDB DOI: 10.2210/pdb1A16/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1997-12-22 Released: 1999-04-06 
• Deposition Author(s): Wilce, M.C., Bond, C.S., Lilley, P.E., Dixon, N.E., Freeman, H.C., Guss, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli.

Wilce, M.C., Bond, C.S., Dixon, N.E., Freeman, H.C., Guss, J.M., Lilley, P.E., Wilce, J.A.

(1998) Proc Natl Acad Sci U S A 95: 3472-3477

• PubMed: 9520390 
• DOI: 10.1073/pnas.95.7.3472
• Primary Citation of Related Structures:  
  1A16, 1JAW


• PubMed Abstract: 
  

The structure of the proline-specific aminopeptidase (EC 3.4.11.9) from Escherichia coli has been solved and refined for crystals of the native enzyme at a 2.0-A resolution, for a dipeptide-inhibited complex at 2.3-A resolution, and for a low-pH inactive form at 2.7-A resolution. The protein crystallizes as a tetramer, more correctly a dimer of dimers, at both high and low pH, consistent with observations from analytical ultracentrifuge studies that show that the protein is a tetramer under physiological conditions. The monomer folds into two domains. The active site, in the larger C-terminal domain, contains a dinuclear manganese center in which a bridging water molecule or hydroxide ion appears poised to act as the nucleophile in the attack on the scissile peptide bond of Xaa-Pro. The metal-binding residues are located in a single subunit, but the residues surrounding the active site are contributed by three subunits. The fold of the protein resembles that of creatine amidinohydrolase (creatinase, not a metalloenzyme). The C-terminal catalytic domain is also similar to the single-domain enzyme methionine aminopeptidase that has a dinuclear cobalt center.

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Organizational Affiliation: 

Department of Biochemistry, University of Sydney, New South Wales 2006, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMINOPEPTIDASE P	A	440	Escherichia coli	Mutation(s): 0  EC: 3.4.11.9
UniProt
Find proteins for P15034 (Escherichia coli (strain K12)) Explore P15034  Go to UniProtKB:  P15034

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LEU	C [auth A]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N
PRO	B [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
MN	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.3	α = 90
b = 177.3	β = 90
c = 96.5	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-12-22 
• Released Date: 1999-04-06 
Deposition Author(s): Wilce, M.C., Bond, C.S., Lilley, P.E., Dixon, N.E., Freeman, H.C., Guss, J.M.

Revision History  

• Version 1.0: 1999-04-06
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance