2JBH

Human phosphoribosyl transferase domain containing 1

• PDB DOI: https://doi.org/10.2210/pdb2JBH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-12-07 Released: 2006-12-20 
• Deposition Author(s): Welin, M., Stenmark, P., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Edwards, A., Eklund, H., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg Schiavone, L., Hogbom, M., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Sundstrom, M., Uppenberg, J., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Structural and Functional Studies of the Human Phosphoribosyltransferase Domain Containing Protein 1.

Welin, M., Egeblad, L., Johansson, A., Stenmark, P., Wang, L., Flodin, S., Nyman, T., Tresaugues, L., Kotenyova, T., Johansson, I., Eriksson, S., Eklund, H., Nordlund, P.

(2010) FEBS J 277: 4920

• PubMed: 21054786 
• DOI: https://doi.org/10.1111/j.1742-4658.2010.07897.x
• Primary Citation of Related Structures:  
  2JBH


• PubMed Abstract: 
  

  Human hypoxanthine-guanine phosphoribosyltransferase (HPRT) (EC 2.4.2.8) catalyzes the conversion of hypoxanthine and guanine to their respective nucleoside monophosphates. Human HPRT deficiency as a result of genetic mutations is linked to both Lesch-Nyhan disease and gout. In the present study, we have characterized phosphoribosyltransferase domain containing protein 1 (PRTFDC1), a human HPRT homolog of unknown function. The PRTFDC1 structure has been determined at 1.7 Å resolution with bound GMP. The overall structure and GMP binding mode are very similar to that observed for HPRT. Using a thermal-melt assay, a nucleotide metabolome library was screened against PRTFDC1 and revealed that hypoxanthine and guanine specifically interacted with the enzyme. It was subsequently confirmed that PRTFDC1 could convert these two bases into their corresponding nucleoside monophosphate. However, the catalytic efficiency (k(cat)/K(m)) of PRTFDC1 towards hypoxanthine and guanine was only 0.26% and 0.09%, respectively, of that of HPRT. This low activity could be explained by the fact that PRTFDC1 has a Gly in the position of the proposed catalytic Asp of HPRT. In PRTFDC1, a water molecule at the position of the aspartic acid side chain position in HPRT might be responsible for the low activity observed by acting as a weak base. The data obtained in the present study indicate that PRTFDC1 does not have a direct catalytic role in the nucleotide salvage pathway.

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Organizational Affiliation: 

Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 52.7 kDa 
• Atom Count: 3,799 
• Modelled Residue Count: 421 
• Deposited Residue Count: 450 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYLTRANSFERASE DOMAIN-CONTAINING PROTEIN 1	A, B	225	Homo sapiens	Mutation(s): 0  Gene Names: PRTFDC1 EC: 2.4.2.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRG1 (Homo sapiens) Explore Q9NRG1  Go to UniProtKB:  Q9NRG1
PHAROS:  Q9NRG1 GTEx:  ENSG00000099256

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	F [auth A], J [auth B]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
PO4	C [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	D [auth A], E [auth A], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS	A, B	L-PEPTIDE LINKING	C5 H12 As N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.232	α = 90
b = 139.232	β = 90
c = 52.132	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-20 
Deposition Author(s): Welin, M., Stenmark, P., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Edwards, A., Eklund, H., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg Schiavone, L., Hogbom, M., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Sundstrom, M., Uppenberg, J., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Nordlund, P.

Revision History  

• Version 1.0: 2006-12-20
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description