2HW4 | pdb_00002hw4

Crystal structure of human phosphohistidine phosphatase

• PDB DOI: https://doi.org/10.2210/pdb2HW4/pdb

• Classification: structural genomics, hydrolase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-31 Released: 2006-08-29 
• Deposition Author(s): Busam, R.D., Thorsell, A.G., Arrowsmith, C., Berglund, H., Collins, R., Edwards, A., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Holmberg Schiavone, L., Hogbom, M., Kotenyova, T., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Ogg, D., Stenmark, P., Sundstrom, M., Uppenberg, J., Van Den Berg, S., Weigelt, J., Persson, C., Hallberg, B.M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.225 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

First structure of a eukaryotic phosphohistidine phosphatase

Busam, R.D., Thorsell, A.G., Flores, A., Persson, C., Hallberg, B.M.

(2006) J Biological Chem 281: 33830-33834

• PubMed: 16990267 
• DOI: https://doi.org/10.1074/jbc.C600231200
• Primary Citation Related Structures: 
  2HW4


• PubMed Abstract: 
  

  Phosphatases are a diverse group of enzymes that regulate numerous cellular processes. Much of what is known relates to the tyrosine, threonine, and serine phosphatases, whereas the histidine phosphatases have not been studied as much. The structure of phosphohistidine phosphatase (PHPT1), the first identified eukaryotic-protein histidine phosphatase, has been determined to a resolution of 1.9A using multiple-wavelength anomalous dispersion methods. This enzyme can dephosphorylate a variety of proteins (e.g. ATP-citrate lyase and the beta-subunit of G proteins). A putative active site has been identified by its electrostatic character, ion binding, and conserved protein residues. Histidine 53 is proposed to play a major role in histidine dephosphorylation based on these observations and previous mutational studies. Models of peptide binding are discussed to suggest possible mechanisms for substrate recognition.

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Organizational Affiliation: 
• Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.95 kDa 
• Atom Count: 1,095 
• Modeled Residue Count: 116 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14 kDa phosphohistidine phosphatase	A	144	Homo sapiens	Mutation(s): 0  Gene Names: PHPT1, PHP14 EC: 3.1.3 (PDB Primary Data), 3.9.1.3 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRX4 (Homo sapiens) Explore Q9NRX4  Go to UniProtKB:  Q9NRX4
GTEx:  ENSG00000054148

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.225 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.53	α = 90
b = 112.53	β = 90
c = 29.37	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-29 
Deposition Author(s): Busam, R.D., Thorsell, A.G., Arrowsmith, C., Berglund, H., Collins, R., Edwards, A., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Holmberg Schiavone, L., Hogbom, M., Kotenyova, T., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Ogg, D., Stenmark, P., Sundstrom, M., Uppenberg, J., Van Den Berg, S., Weigelt, J., Persson, C., Hallberg, B.M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description