5NNA | pdb_00005nna

Isatin hydrolase A (IHA) from Labrenzia aggregata bound to benzyl benzoate

• PDB DOI: https://doi.org/10.2210/pdb5NNA/pdb

• Classification: HYDROLASE
• Organism(s): Roseibium aggregatum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-08 Released: 2018-05-16 
• Deposition Author(s): Sommer, T., Bjerregaard-Andersen, K., Morth, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase.

Sommer, T., Bjerregaard-Andersen, K., Uribe, L., Etzerodt, M., Diezemann, G., Gauss, J., Cascella, M., Morth, J.P.

(2018) Sci Rep 8: 13104-13104

• PubMed: 30166577 
• DOI: https://doi.org/10.1038/s41598-018-31259-y
• Primary Citation Related Structures: 
  5NMP, 5NNA, 5NNB


• PubMed Abstract: 
  

  The catalytic mechanism of the cyclic amidohydrolase isatin hydrolase depends on a catalytically active manganese in the substrate-binding pocket. The Mn ²⁺ ion is bound by a motif also present in other metal dependent hydrolases like the bacterial kynurenine formamidase. The crystal structures of the isatin hydrolases from Labrenzia aggregata and Ralstonia solanacearum combined with activity assays allow for the identification of key determinants specific for the reaction mechanism. Active site residues central to the hydrolytic mechanism include a novel catalytic triad Asp-His-His supported by structural comparison and hybrid quantum mechanics/classical mechanics simulations. A hydrolytic mechanism for a Mn ²⁺ dependent amidohydrolases that disfavour Zn ²⁺ as the primary catalytically active site metal proposed here is supported by these likely cases of convergent evolution. The work illustrates a fundamental difference in the substrate-binding mode between Mn ²⁺ dependent isatin hydrolase like enzymes in comparison with the vast number of Zn ²⁺ dependent enzymes.

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Organizational Affiliation: 
• Norwegian Center for Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway.
Department of Chemistry, University of Oslo, Sem Sælands vei 26, 0371, Oslo, Norway.
Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.
Graduate School Materials Science in Mainz, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, 55128, Mainz, Germany.
Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10C, 8000, Aarhus, Denmark.
Department of Chemistry, University of Oslo, Sem Sælands vei 26, 0371, Oslo, Norway. [e-mail].
Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Sem Saelands vei 26, 0371, Oslo, Norway. [e-mail].
Norwegian Center for Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway. [e-mail].
Institute for Experimental Medical Research, Oslo University Hospital, 0424, Oslo, Norway. [e-mail].
Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 116.86 kDa 
• Atom Count: 9,195 
• Modeled Residue Count: 1,032 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
isatin hydrolase A	A, B, C, D	264	Roseibium aggregatum	Mutation(s): 0  Gene Names: SIAM614_30646
UniProt
Find proteins for A0P0F0 (Roseibium aggregatum (strain ATCC 25650 / DSM 13394 / JCM 20685 / NBRC 16684 / NCIMB 2208 / IAM 12614 / B1)) Explore A0P0F0  Go to UniProtKB:  A0P0F0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	J [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
BZM	E [auth A], H [auth B], L [auth C], N [auth D]	BENZOIC ACID PHENYLMETHYLESTER C14 H12 O2 SESFRYSPDFLNCH-UHFFFAOYSA-N
BTB	G [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
PEG	K [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MN	F [auth A], I [auth B], M [auth C], O [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.69	α = 108.23
b = 70.67	β = 95.94
c = 92.92	γ = 101.48

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Sommer, T., Bjerregaard-Andersen, K., Morth, J.P.

Revision History  

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description