7D2F | pdb_00007d2f

Lp major histidine acid phosphatase mutant D281A/5'-AMP

• PDB DOI: https://doi.org/10.2210/pdb7D2F/pdb

• Classification: HYDROLASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-09-16 Released: 2021-09-22 
• Deposition Author(s): Guo, Y., Teng, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.256 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structural insights into a new substrate binding mode of a histidine acid phosphatase from Legionella pneumophila.

Guo, Y., Zhou, D., Zhang, H., Zhang, N.N., Qi, X., Chen, X., Chen, Q., Li, J., Ge, H., Teng, Y.B.

(2021) Biochem Biophys Res Commun 540: 90-94

• PubMed: 33450485 
• DOI: https://doi.org/10.1016/j.bbrc.2020.12.070
• Primary Citation Related Structures: 
  7D2F, 7DOQ


• PubMed Abstract: 
  

  MapA is a histidine acid phosphatase (HAP) from Legionella pneumophila that catalyzes the hydroxylation of a phosphoryl group from phosphomonoesters by an active-site histidine. Several structures of HAPs, including MapA, in complex with the inhibitor tartrate have been solved and the substrate binding tunnel identified; however, the substrate recognition mechanism remains unknown. To gain insight into the mechanism of substrate recognition, the crystal structures of apo-MapA and the MapA ^D281A mutant in complex with 5'-AMP were solved at 2.2 and 2.6 Å resolution, respectively. The structure of the MapA ^D281A /5'-AMP complex reveals that the 5'-AMP fits fully into the substrate binding tunnel, with the 2'-hydroxyl group of the ribose moiety stabilized by Glu201 and the adenine moiety sandwiched between His205 and Phe237. This is the second structure of a HAP/AMP complex solved with 5'-AMP binding in a unique manner in the active site. The structure presents a new substrate recognition mechanism of HAPs.

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Organizational Affiliation: 
• School of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China. Electronic address: [e-mail].
Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui, 230601, People's Republic of China. Electronic address: [e-mail].
School of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China. Electronic address: [e-mail].
Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui, 230601, People's Republic of China. Electronic address: [e-mail].
Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, People's Republic of China. Electronic address: [e-mail].
Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui, 230601, People's Republic of China. Electronic address: [e-mail].
School of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China. Electronic address: [e-mail].
School of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China. Electronic address: [e-mail].
Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui, 230601, People's Republic of China. Electronic address: [e-mail].
School of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China. Electronic address: [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)

Macromolecule Content 

• Total Structure Weight: 74.28 kDa 
• Atom Count: 5,231 
• Modeled Residue Count: 654 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major acid phosphatase	A, B	328	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 1  Gene Names: lpg1119 EC: 3.1.3.2
UniProt
Find proteins for Q5ZWG6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZWG6  Go to UniProtKB:  Q5ZWG6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	C [auth A], D [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.256 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.61	α = 90
b = 118.41	β = 90
c = 118.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-22 
Deposition Author(s): Guo, Y., Teng, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31700650

Revision History  

• Version 1.0: 2021-09-22
  Type: Initial release
  
• Version 1.1: 2022-07-06
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary