ISDA

Deposition Date 2004-01-14

Release Date 2004-04-06

Last Version Date 2023-11-15

Entry Detail

PDB ID:

1S3T

Keywords:

HYDROLASE

Title:

BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE

Biological Source:

Source Organism:

Sporosarcina pasteurii (Taxon ID: 1474)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.10 Å

R-Value Free:

0.20

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 63 2 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Urease gamma subunit
Gene (Uniprot):ureA
Chain IDs:A
Chain Length:100
Number of Molecules:1
Biological Source:Sporosarcina pasteurii

UniProt ID:P41022 Pfam ID:PF00547 EC:3.5.1.5

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Urease beta subunit
Gene (Uniprot):ureB
Chain IDs:B
Chain Length:126
Number of Molecules:1
Biological Source:Sporosarcina pasteurii

UniProt ID:P41021 Pfam ID:PF00699 EC:3.5.1.5

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Urease alpha subunit
Gene (Uniprot):ureC
Chain IDs:C
Chain Length:570
Number of Molecules:1
Biological Source:Sporosarcina pasteurii

UniProt ID:P41020 Pfam ID:PF00449, PF01979 EC:3.5.1.5

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
CXM	A	MET	N-CARBOXYMETHIONINE
KCX	C	LYS	LYSINE NZ-CARBOXYLIC ACID

Ligand Molecules

BO3

SO4

Primary Citation

Molecular Details of Urease Inhibition by Boric Acid: Insights into the Catalytic Mechanism.

Benini, S, Rypniewski, W.R, Wilson, K.S, Mangani, S, Ciurli, S, Benini, S, Rypniewski, W.R, Wilson, K.S, Ciurli, S, Mangani, S, Benini, S, Rypniewski, W.R, Wilson, K.S, Miletti, S, Ciurli, S, Mangani, S, Benini, S, Rypniewski, W.R, Wilson, K.S, Miletti, S, Ciurli, S, Mangani, S, Benini, S, Ciurli, S, Rypniewski, W.R, Wilson, K.S, Mangani, S, Benini, S, Ciurli, S, Rypniewski, W.R, Wilson, K.S, Mangani, S.Show

J.Am.Chem.Soc. 126 3714 3715 (2004)

PMID: 15038715 DOI: 10.1021/ja049618p

Abstact

The structure of the complex of urease, a Ni-containing metalloenzyme, with boric acid was determined at 2.10 A resolution. The complex shows the unprecedented binding mode of the competitive inhibitor to the dinuclear metal center, with the B(OH)3 molecule bridging the Ni ions and leaving in place the bridging hydroxide. Boric acid can be considered a substrate analogue of urea, and the structure supports the proposal that the Ni-bridging hydroxide acts as the nucleophile in the enzymatic process of urea hydrolysis.

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Primary Citation of related structures