9IVY | pdb_00009ivy

Pseudomonas aeruginosa Histidinol dehydrogenase with NADH and Zn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.243 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure-guided revelation of metal ion-dependent functional ambiguity in Pseudomonas aeruginosa histidinol dehydrogenase.

Basu Choudhury, G.Chatterjee, R.Saha, A.Sarkar, D.J.Das, B.K.Datta, S.

(2025) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70209
  • Primary Citation of Related Structures:  
    8XSQ, 9IVY, 9LBV

  • PubMed Abstract: 

    Histidinol dehydrogenase (HisD) is an enzyme that catalyzes the final step in histidine biosynthesis, converting l-histidinol to l-histidine, and plays a crucial role in bacterial metabolism. In this study, we investigated the ambiguity in catalytic mechanisms of the HisD enzyme in Pseudomonas aeruginosa using biochemical and structural approaches, particularly through X-ray crystallography. The primary objective of this research was to explore the structural and functional variability of PaHisD and provide knowledge for potential therapeutic developments in this organism. Our findings reveal significant structural alterations in the enzyme as we identified a new substrate-binding pocket due to structural rearrangements. We also confirmed the presence of an additional metal ion (Zn 2+ ), contributing to its catalytic ambiguity. Given its relevance in molecular drug targeting, we examined how the differences in NAD + and substrate binding could impact the efficacy of existing inhibitors. Computational studies further evaluated the variability in inhibitor binding, providing new insights for designing more effective therapeutic agents targeting PaHisD.


  • Organizational Affiliation
    • CSIR-Indian Institute of Chemical Biology, Kolkata, India.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histidinol dehydrogenase
A, B
440Pseudomonas aeruginosaMutation(s): 0 
Gene Names: hisDCAZ10_21075IPC1295_15380PA52Ts2_1476PAERUG_P19_London_7_VIM_2_05_10_06424
EC: 1.1.1.23
UniProt
Find proteins for Q9HVW9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HVW9 
Go to UniProtKB:  Q9HVW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HVW9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
H [auth B]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
I [auth B],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.243 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.299α = 90
b = 89.527β = 90
c = 139.871γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Council of Scientific & Industrial Research (CSIR)India--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references