Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 24.64 kDa 
• Atom Count: 2073 
• Modelled Residue Count: 202 
• Deposited Residue Count: 202 
• Unique protein chains: 1

4W79

Crystal Structure of Human Protein N-terminal Glutamine Amidohydrolase

• PDB DOI: 10.2210/pdb4W79/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-08-21 Released: 2014-09-17 
• Deposition Author(s): Bitto, E., Bingman, C.A., McCoy, J.G., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.170 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3C9Q

Literature

Crystal structure of human protein N-terminal glutamine amidohydrolase, an initial component of the N-end rule pathway.

Park, M.S., Bitto, E., Kim, K.R., Bingman, C.A., Miller, M.D., Kim, H.J., Han, B.W., Phillips, G.N.

(2014) PLoS One 9: e111142-e111142

• PubMed: 25356641 
• DOI: 10.1371/journal.pone.0111142
• Primary Citation of Related Structures:  
  4W79


• PubMed Abstract: 
  

The N-end rule states that half-life of protein is determined by their N-terminal amino acid residue. N-terminal glutamine amidohydrolase (Ntaq) converts N-terminal glutamine to glutamate by eliminating the amine group and plays an essential role in the N-end rule pathway for protein degradation. Here, we report the crystal structure of human Ntaq1 bound with the N-terminus of a symmetry-related Ntaq1 molecule at 1.5 Å resolution. The structure reveals a monomeric globular protein with alpha-beta-alpha three-layer sandwich architecture. The catalytic triad located in the active site, Cys-His-Asp, is highly conserved among Ntaq family and transglutaminases from diverse organisms. The N-terminus of a symmetry-related Ntaq1 molecule bound in the substrate binding cleft and the active site suggest possible substrate binding mode of hNtaq1. Based on our crystal structure of hNtaq1 and docking study with all the tripeptides with N-terminal glutamine, we propose how the peptide backbone recognition patch of hNtaq1 forms nonspecific interactions with N-terminal peptides of substrate proteins. Upon binding of a substrate with N-terminal glutamine, active site catalytic triad mediates the deamination of the N-terminal residue to glutamate by a mechanism analogous to that of cysteine proteases.

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Organizational Affiliation: 

Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin, United States of America; Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein N-terminal glutamine amidohydrolase	A	202	Homo sapiens	Mutation(s): 4  Gene Names: WDYHV1, C8orf32, NTAQ1 EC: 3.5.1 (PDB Primary Data), 3.5.1.122 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HA8 (Homo sapiens) Explore Q96HA8  Go to UniProtKB:  Q96HA8
PHAROS:  Q96HA8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	P [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO3	M [auth A], N [auth A], O [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.170 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.322	α = 90
b = 64.039	β = 90
c = 113.66	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-08-21 
• Released Date: 2014-09-17 
Deposition Author(s): Bitto, E., Bingman, C.A., McCoy, J.G., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54 GM074901

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence