6A0H: Crystal Structure Of Human Protein N-terminal ... - RCSB PDB

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227,933 Structures from the PDB 1,068,577 Computed Structure Models (CSM)

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Data API 6A0H

Crystal structure of human protein N-terminal asparagine amidohydrolase (NTAN1) C75S mutant with Asn-Leu-Ala-Ala-Arg peptide

• PDB DOI: https://doi.org/10.2210/pdb6A0H/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 
• Deposited: 2018-06-05 Released: 2019-12-11 
• Deposition Author(s): Park, J.S., Han, B.W.
• Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.242 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Starting Model: experimentalView more details

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history. LiteratureDownload Primary Citation 

•  Download Mendeley

Structural Analyses on the Deamidation of N-Terminal Asn in the Human N-Degron Pathway.

Park, J.S., Lee, J.Y., Nguyen, Y.T.K., Kang, N.W., Oh, E.K., Jang, D.M., Kim, H.J., Kim, D.D., Han, B.W.

(2020) Biomolecules 10

• PubMed: 31968674 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.3390/biom10010163
• Primary Citation of Related Structures:  6A0E, 6A0F, 6A0H, 6A0I
• PubMed Abstract: 

  The N-degron pathway is a proteolytic system in which a single N-terminal amino acid acts as a determinant of protein degradation. Especially, degradation signaling of N-terminal asparagine (Nt-Asn) in eukaryotes is initiated from its deamidation by N-terminal asparagine amidohydrolase 1 (NTAN1) into aspartate. Here, we have elucidated structural principles of deamidation by human NTAN1. NTAN1 adopts the characteristic scaffold of CNF1/YfiH-like cysteine hydrolases that features an α-β-β sandwich structure and a catalytic triad comprising Cys, His, and Ser. In vitro deamidation assays using model peptide substrates with varying lengths and sequences showed that NTAN1 prefers hydrophobic residues at the second-position. The structures of NTAN1-peptide complexes further revealed that the recognition of Nt-Asn is sufficiently organized to produce high specificity, and the side chain of the second-position residue is accommodated in a hydrophobic pocket adjacent to the active site of NTAN1. Collectively, our structural and biochemical analyses of the substrate specificity of NTAN1 contribute to understanding the structural basis of all three amidases in the eukaryotic N-degron pathway.

   View More
Organizational Affiliation: 

Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea.

Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (PO4)

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (PO4)

Global Symmetry: Asymmetric - C1 Global Stoichiometry: Hetero 2-mer - A1B1 LessFind Similar Assemblies

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

Biological Assembly Evidence: gel filtrationBiological Assembly 2  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (PO4)

Global Symmetry: Asymmetric - C1 Global Stoichiometry: Hetero 2-mer - A1B1 LessFind Similar Assemblies

Biological assembly 2 assigned by authors and generated by PISA (software)

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Macromolecule Content

• Total Structure Weight: 73.68 kDa 
• Atom Count: 4,895 
• Modelled Residue Count: 611 
• Deposited Residue Count: 646 
• Unique protein chains: 2

MacromoleculesFind similar proteins by: Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein N-terminal asparagine amidohydrolase	A, B	318	Homo sapiens	Mutation(s): 1 Gene Names: NTAN1EC: 3.5.1 (PDB Primary Data), 3.5.1.121 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96AB6 (Homo sapiens)Explore Q96AB6 Go to UniProtKB:  Q96AB6
PHAROS:  Q96AB6GTEx:  ENSG00000157045
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96AB6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5-mer peptide ASN-LEU-ALA-ALA-ARG	C, D	5	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4Query on PO4Download Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	H [auth A]I [auth A]J [auth A]M [auth B]N [auth B]H [auth A],I [auth A],J [auth A],M [auth B],N [auth B],O [auth B] Less	PHOSPHATE IONO4 PNBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
GOLQuery on GOLDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	E [auth A],F [auth A],G [auth A],K [auth B],L [auth B]	GLYCEROLC3 H8 O3PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.242 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 21 21 21

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.003	α = 90
b = 85.884	β = 90
c = 88.094	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental dataEntry History & Funding Information

Deposition Data

• Released Date: 2019-12-11 
Deposition Author(s): Park, J.S., Han, B.W.

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	2011-0030001
National Research Foundation (Korea)	Korea, Republic Of	2013M-3A6A-4043695

Revision History (Full details and data files)

• Version 1.0: 2019-12-11Type: Initial release
• Version 1.1: 2020-06-24Changes: Database references
• Version 1.2: 2023-11-22Changes: Data collection, Database references, Refinement description

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