1WAR

Recombinant Human Purple Acid Phosphatase expressed in Pichia Pastoris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of Recombinant Human Purple Acid Phosphatase with and without an Inhibitory Conformation of the Repression Loop.

Strater, N.Jasper, B.Scholte, M.Krebs, B.Duff, A.P.Langley, D.B.Han, R.Averill, B.A.Freeman, H.C.Guss, J.M.

(2005) J Mol Biol 351: 233

  • DOI: 10.1016/j.jmb.2005.04.014
  • Primary Citation of Related Structures:  
    1WAR, 2BQ8

  • PubMed Abstract: 
  • The crystal structure of human purple acid phosphatase recombinantly expressed in Escherichia coli (rHPAP(Ec)) and Pichia pastoris (rHPAP(Pp)) has been determined in two different crystal forms, both at 2.2A resolution. In both cases, the enzyme crystallized in its oxidized (inactive) state, in which both Fe atoms in the dinuclear active site are Fe(III) ...

    The crystal structure of human purple acid phosphatase recombinantly expressed in Escherichia coli (rHPAP(Ec)) and Pichia pastoris (rHPAP(Pp)) has been determined in two different crystal forms, both at 2.2A resolution. In both cases, the enzyme crystallized in its oxidized (inactive) state, in which both Fe atoms in the dinuclear active site are Fe(III). The main difference between the two structures is the conformation of the enzyme "repression loop". Proteolytic cleavage of this loop in vivo or in vitro results in significant activation of the mammalian PAPs. In the crystals obtained from rHPAP(Ec), the carboxylate side-chain of Asp145 of this loop acts as a bidentate ligand that bridges the two metal atoms, in a manner analogous to a possible binding mode for a phosphate ester substrate in the enzyme-substrate complex. The carboxylate side-chain of Asp145 and the neighboring Phe146 side-chain thus block the active site, thereby inactivating the enzyme. In the crystal structure of rHPAP(Pp), the enzyme "repression loop" has an open conformation similar to that observed in other mammalian PAP structures. The present structures demonstrate that the repression loop exhibits significant conformational flexibility, and the observed alternate binding mode suggests a possible inhibitory role for this loop.


    Organizational Affiliation

    Biotechnologisch-Biomedizinisches Zentrum, Fakultät für Chemie und Mineralogie der Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN PURPLE ACID PHOSPHATASEA310Homo sapiensMutation(s): 0 
Gene Names: ACP5
EC: 3.1.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P13686 (Homo sapiens)
Explore P13686 
Go to UniProtKB:  P13686
PHAROS:  P13686
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.141 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.538α = 90
b = 80.538β = 90
c = 99.998γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2019-04-03
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary