8HUC

Crystal structure of PaIch (Pec1)

PDB DOI: https://doi.org/10.2210/pdb8HUC/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Pseudomonas aeruginosa UCBPP-PA14
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-12-23 Released: 2023-12-27
Deposition Author(s): Pramanik, A., Datta, S.
Funding Organization(s): Council of Scientific & Industrial Research (CSIR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.221
R-Value Work: 0.182
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural and functional insights of itaconyl-CoA hydratase from Pseudomonas aeruginosa highlight a novel N-terminal hotdog fold.

Pramanik, A., Datta, S.

(2024) FEBS Lett 598: 1387-1401

PubMed: 38575551 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.14867
Primary Citation of Related Structures:
8HUC

PubMed Abstract:
Itaconyl-CoA hydratase in Pseudomonas aeruginosa (PaIch) converts itaconyl-CoA to (S)-citramalyl-CoA upon addition of a water molecule, a part of an itaconate catabolic pathway in virulent organisms required for their survival in humans host cells. Crystal structure analysis of PaIch showed that a unique N-terminal hotdog fold containing a 4-residue short helical segment α3-, named as an "eaten sausage", followed by a flexible loop region slipped away from the conserved β-sheet scaffold, whereas the C-terminal hotdog fold is similar to all MaoC. A conserved hydratase motif with catalytic residues provides mechanistic insights into catalysis, and existence of a longer substrate binding tunnel may suggest the binding of longer CoA derivatives.

Organizational Affiliation

Department of Structural Biology and Bio-informatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India.

Macromolecule Content

Total Structure Weight: 123.83 kDa
Atom Count: 9,321
Modelled Residue Count: 1,037
Deposited Residue Count: 1,100
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MaoC_dehydrat_N domain-containing protein	A, B, C, D	275	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0 Gene Names: PA14_52910
UniProt
Find proteins for A0A0H2Z790 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore A0A0H2Z790 Go to UniProtKB: A0A0H2Z790
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2Z790
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D]	E [auth A] G [auth A] J [auth A] P [auth B] Q [auth B] E [auth A], G [auth A], J [auth A], P [auth B], Q [auth B], S [auth C], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain X [auth D]
NO3 (Subject of Investigation/LOI) Query on NO3 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D]	F [auth A] H [auth A] I [auth A] K [auth B] L [auth B] F [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], R [auth C], T [auth C], U [auth C], V [auth C], W [auth C], Y [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D]