1FDP

PROENZYME OF HUMAN COMPLEMENT FACTOR D, RECOMBINANT PROFACTOR D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of profactor D activation: from a highly flexible zymogen to a novel self-inhibited serine protease, complement factor D.

Jing, H.Macon, K.J.Moore, D.DeLucas, L.J.Volanakis, J.E.Narayana, S.V.

(1999) EMBO J 18: 804-814

  • DOI: 10.1093/emboj/18.4.804
  • Primary Citation of Related Structures:  
    1FDP

  • PubMed Abstract: 
  • The crystal structure of profactor D, determined at 2.1 A resolution with an Rfree and an R-factor of 25.1 and 20.4%, respectively, displays highly flexible or disordered conformation for five regions: N-22, 71-76, 143-152, 187-193 and 215-223. A com ...

    The crystal structure of profactor D, determined at 2.1 A resolution with an Rfree and an R-factor of 25.1 and 20.4%, respectively, displays highly flexible or disordered conformation for five regions: N-22, 71-76, 143-152, 187-193 and 215-223. A comparison with the structure of its mature serine protease, complement factor D, revealed major conformational changes in the similar regions. Comparisons with the zymogen-active enzyme pairs of chymotrypsinogen, trypsinogen and prethrombin-2 showed a similar distribution of the flexible regions. However, profactor D is the most flexible of the four, and its mature enzyme displays inactive, self-inhibited active site conformation. Examination of the surface properties of the N-terminus-binding pocket indicates that Ile16 may play the initial positioning role for the N-terminus, and Leu17 probably also helps in inducing the required conformational changes. This process, perhaps shared by most chymotrypsinogen-like zymogens, is followed by a factor D-unique step, the re-orientation of an external Arg218 to an internal position for salt-bridging with Asp189, leading to the generation of the self-inhibited factor D.


    Related Citations: 
    • Structures of Native and Complexed Complement Factor D: Implications of the Atypical His57 Conformation and Self-Inhibitory Loop in the Regulation of Specific Serine Protease Activity
      Jing, H., Babu, Y.S., Moore, D., Kilpatrick, J.M., Liu, X.-Y., Volanakis, J.E., Narayana, S.V.L.
      (1998) J Mol Biol 282: 1061
    • Complement Factor D, a Novel Serine Protease
      Volanakis, J.E., Narayana, S.V.L.
      (1996) Protein Sci 5: 553
    • Structure of Human Factor D. A Complement System Protein at 2.0 A Resolution
      Narayana, S.V.L., Carson, M., El-Kabbani, O., Kilpatrick, J.M., Moore, D., Chen, X., Bugg, C.E., Volanakis, J.E., Delucas, L.J.
      (1994) J Mol Biol 235: 695
    • Preliminary Crystallographic Studies on Human Complement Profactor D
      Narayana, S.V.L., Yamauchi, Y., Macon, K.J., Moore, D., Delucas, L.J., Volanakis, J.E.
      (1994) J Mol Biol 235: 1144

    Organizational Affiliation

    Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROENZYME OF COMPLEMENT FACTOR DABCD235Homo sapiensMutation(s): 0 
Gene Names: CFDDFPFD
EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens)
Explore P00746 
Go to UniProtKB:  P00746
NIH Common Fund Data Resources
PHAROS  P00746
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.05α = 90
b = 70.32β = 101.98
c = 86.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-03
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-12-07
    Changes: Database references