1E9Z Hydrolase date Nov 01, 2000
title Crystal Structure Of Helicobacter Pylori Urease
authors N.-C.Ha, S.-T.Oh, B.-H.Oh
compound source
Molecule: Urease Alpha Subunit
Chain: A
Engineered: Yes
Ec: 3.5.1.5
 Organism_scientific: Helicobacter Pylori
Expression_system: Escherichia Coli

Molecule: Urease Beta Subunit
Chain: B
Engineered: Yes
Organism_scientific: Helicobacter Pylori
Expression_system: Escherichia Coli
symmetry Space Group: I 2 3
R_factor 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
177.910 177.910 177.910 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.0 Å
ligand KCX, NI enzyme Urease. Hydrolase E.C.3.5.1.5 BRENDA
note 1E9Z is a representative structure
similarity In the n-terminal section; belongs to the urease gamma subunit family. Belongs to the urease family. In the c-terminal section; belongs to the urease beta subunit family.[Amidohydro_1]
subunit Heterohexamer of 3 alpha and 3 beta subunits. Four heterohexamers assemble to form a 16 nm spherical complex.
catalytic activ. Urea + h(2)o = co(2) + 2 nh(3).
post-translat. modifications Lys-219 is carbamylated. The carbamoyl group provides the ligands for the two nickel ions (by similarity).
subcellular loc. Cytoplasm.
genes ureA, ureB, ureC (B. pasteurii); ureA, ureB (H. pylori); ureA, ureB, ureC (K. aerogenes)
Gene
Ontology
ChainFunctionProcessComponent
A
  • urease activity
  • nickel ion binding
  • hydrolase activity
  • nitrogen compound metabolic ...
  • cytoplasm
    • B
  • urease activity
  • nickel ion binding
  • hydrolase activity
  • metal ion binding
  • nitrogen compound metabolic ...
  • urea metabolic process

    • Primary referenceSupramolecular assembly and acid resistance of Helicobacter pylori urease., Ha NC, Oh ST, Sung JY, Cha KA, Lee MH, Oh BH, Nat Struct Biol 2001 Jun;8(6):505-9. PMID:11373617
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (1e9z.pdb1.gz) 1470 Kb
  • CSU: Contacts of Structural Units for 1E9Z
  • Likely Quarternary Molecular Structure file(s) for 1E9Z
  • Retrieve 1E9Z in mmCIF format [Save to disk]
    • View 1E9Z in 3D
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • On AstexViewer, from MSD-EBI (viewer documentation).
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    • Visual 3D analysis of 1E9Z
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    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1E9Z, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1e9za2, region A:1-105 [Jmol] [rasmolscript] [script source]
        - Domain d1e9za1, region A:106-238 [Jmol] [rasmolscript] [script source]
        - Domain d1e9zb1, region B:1-131,B:432-480 [Jmol] [rasmolscript] [script source]
        - Domain d1e9zb2, region B:132-431,B:481-569 [Jmol] [rasmolscript] [script source]
  • Fold representative 1e9z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1e9z_A] [1e9z_B]
    • Other resources with information on 1E9Z
  • InterPro: IPR002019 , IPR005848 , IPR008223 , IPR006680 , IPR008295 , IPR002026 , IPR011612
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
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