1WAR | pdb_00001war

Recombinant Human Purple Acid Phosphatase expressed in Pichia Pastoris


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.22 Å
  • R-Value Free:&nbsp
    0.198 (Depositor), 0.204 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.138 (Depositor)&nbsp
  • R-Value Observed:&nbsp
    0.141&nbsp(Depositor)&nbsp

Starting Model: experimental
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This is version 1.5 of the entry. See complete&nbsphistory.&nbsp


Literature

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

Strater, N.,&nbspJasper, B.,&nbspScholte, M.,&nbspKrebs, B.,&nbspDuff, A.P.,&nbspLangley, D.B.,&nbspHan, R.,&nbspAverill, B.A.,&nbspFreeman, H.C.,&nbspGuss, J.M.

(2005) J Mol Biology&nbsp351: 233

  • DOI:&nbsphttps://doi.org/10.1016/j.jmb.2005.04.014
  • Primary Citation Related Structures:&nbsp
    1WAR, 2BQ8

  • PubMed Abstract:&nbsp

    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:&nbsp
    • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HUMAN PURPLE ACID PHOSPHATASE310Homo sapiensMutation(s): 0&nbsp
EC:&nbsp3.1.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP13686&nbsp(Homo sapiens)
Explore&nbspP13686&nbsp
Go to UniProtKB: &nbspP13686
PHAROS: &nbspP13686
GTEx: &nbspENSG00000102575&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13686
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P13686-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.22 Å
  • R-Value Free:&nbsp 0.198 (Depositor), 0.204 (DCC)&nbsp
  • R-Value Work:&nbsp 0.138 (Depositor)&nbsp
  • R-Value Observed:&nbsp0.141&nbsp(Depositor)&nbsp
Space Group:&nbspP 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

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Ligand Structure Quality Assessment&nbsp


Entry History&nbsp

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
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-20
    Changes: Structure summary