2E85

Crystal Structure of the Hydrogenase 3 Maturation protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of hydrogenase maturating endopeptidase HycI from Escherichia coli

Kumarevel, T.Tanaka, T.Bessho, Y.Shinkai, A.Yokoyama, S.

(2009) Biochem.Biophys.Res.Commun. 389: 310-314

  • DOI: 10.1016/j.bbrc.2009.08.135

  • PubMed Abstract: 
  • The maturation of [NiFe]-hydrogenases is a catalyzed process involving the activities of at least seven proteins. The last step consists of the endoproteolytic cleavage of the precursor of the large subunit, after the [NiFe]-metal center has been ass ...

    The maturation of [NiFe]-hydrogenases is a catalyzed process involving the activities of at least seven proteins. The last step consists of the endoproteolytic cleavage of the precursor of the large subunit, after the [NiFe]-metal center has been assembled. The HycI endopeptidase is involved in the C-terminal processing of HycE, the large subunit of hydrogenase 3 from Escherichia coli. Although HycI has been well characterized biochemically, the crystallization of the protein has been quite challenging. Here, we present the crystal structure of HycI at 1.70 A resolution. The crystal structure resembles the recently reported solution structure (NMR) of the same protein and the holo-HyPD structure of the same family, but a significant conformational change is observed at the L5 loop, as compared with the solution structures of HycI and HyPD. In our crystal structure, three specific metal binding sites (Ca1-3) were identified and these metal ions are possibly involved in the C-terminal cleavage of HycE.


    Organizational Affiliation

    RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan. tskvel@spring8.or.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase 3 maturation protease
A, B
159Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: hycI
EC: 3.4.23.51
Find proteins for P0AEV9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEV9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.425α = 90.00
b = 54.984β = 90.00
c = 67.964γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SOLVEphasing
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance