5AHE | pdb_00005ahe

Crystal structure of Salmonella enterica HisA

• PDB DOI: https://doi.org/10.2210/pdb5AHE/pdb

• Classification: ISOMERASE
• Organism(s): Salmonella enterica
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-02-05 Released: 2015-09-02 
• Deposition Author(s): Soderholm, A., Guo, X., Newton, M.S., Evans, G.B., Nasvall, J., Patrick, W.M., Selmer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Two-Step Ligand Binding in a Beta/Alpha8 Barrel Enzyme -Substrate-Bound Structures Shed New Light on the Catalytic Cycle of Hisa

Soderholm, A., Guo, X., Newton, M.S., Evans, G.B., Nasvall, J., Patrick, W.M., Selmer, M.

(2015) J Biological Chem 290: 24657

• PubMed: 26294764 
• DOI: https://doi.org/10.1074/jbc.M115.678086
• Primary Citation Related Structures: 
  5A5W, 5AHE, 5AHF


• PubMed Abstract: 
  

  HisA is a (βα)8 barrel enzyme that catalyzes the Amadori rearrangement of N'-[(5'-phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (ProFAR) to N'-((5'-phosphoribulosyl) formimino)-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) in the histidine biosynthesis pathway, and it is a paradigm for the study of enzyme evolution. Still, its exact catalytic mechanism has remained unclear. Here, we present crystal structures of wild type Salmonella enterica HisA (SeHisA) in its apo-state and of mutants D7N and D7N/D176A in complex with two different conformations of the labile substrate ProFAR, which was structurally visualized for the first time. Site-directed mutagenesis and kinetics demonstrated that Asp-7 acts as the catalytic base, and Asp-176 acts as the catalytic acid. The SeHisA structures with ProFAR display two different states of the long loops on the catalytic face of the structure and demonstrate that initial binding of ProFAR to the active site is independent of loop interactions. When the long loops enclose the substrate, ProFAR adopts an extended conformation where its non-reacting half is in a product-like conformation. This change is associated with shifts in a hydrogen bond network including His-47, Asp-129, Thr-171, and Ser-202, all shown to be functionally important. The closed conformation structure is highly similar to the bifunctional HisA homologue PriA in complex with PRFAR, thus proving that structure and mechanism are conserved between HisA and PriA. This study clarifies the mechanistic cycle of HisA and provides a striking example of how an enzyme and its substrate can undergo coordinated conformational changes before catalysis.

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Organizational Affiliation: 
• From the Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, 751 24 Uppsala, Sweden.
the Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.
the Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33346, Petone, Lower Hutt 5046, New Zealand, and.
the Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, 751 23 Uppsala, Sweden.
the Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand, [e-mail].
From the Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, 751 24 Uppsala, Sweden, [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 27.94 kDa 
• Atom Count: 1,983 
• Modeled Residue Count: 231 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase	A	253	Salmonella enterica	Mutation(s): 0  Gene Names:  hisA, AIY46_13150, AL463_17045, CQW68_13095, D3346_17640, D3Q81_15095, EAW95_14430, FJR52_10950, GCH85_22590, NCTC6385_02080, ND68_15100 EC: 5.3.1.16
UniProt
Find proteins for P10372 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P10372  Go to UniProtKB:  P10372

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PO4	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.769	α = 90
b = 86.769	β = 90
c = 121.53	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Soderholm, A., Guo, X., Newton, M.S., Evans, G.B., Nasvall, J., Patrick, W.M., Selmer, M.

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2015-10-21
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.3: 2024-11-06
  Changes: Structure summary