Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 202.38 kDa 
• Atom Count: 16013 
• Residue Count: 1651 
• Unique protein chains: 1

1NE7

HUMAN GLUCOSAMINE-6-PHOSPHATE DEAMINASE ISOMERASE AT 1.75 A RESOLUTION COMPLEXED WITH N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AND 2-DEOXY-2-AMINO-GLUCITOL-6-PHOSPHATE

• DOI: 10.2210/pdb1NE7/pdb
• Entry: 1NE7 supersedes: 1D9T

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-12-10 Released: 2003-09-23 
• Deposition Author(s): Arreola, R., Valderrama, B., Morante, M.L., Horjales, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.217 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Two mammalian glucosamine-6-phosphate deaminases: a structural and genetic study.

Arreola, R., Valderrama, B., Morante, M.L., Horjales, E.

(2003) FEBS Lett 551: 63-70

• PubMed: 12965206 
• DOI: 10.1016/s0014-5793(03)00896-2
• Primary Citation of Related Structures:  
  1NE7


• PubMed Abstract: 
  

Glucosamine-6-phosphate deaminase (EC 3.5.99.6) is an allosteric enzyme that catalyzes the reversible conversion of D-glucosamine-6-phosphate into D-fructose-6-phosphate and ammonium. Here we describe the existence of two mammalian glucosamine-6-phosphate deaminase enzymes. We present the crystallographic structure of one of them, the long human glucosamine-6-phosphate deaminase, at 1.75 A resolution. Crystals belong to the space group P2(1)2(1)2(1) and present a whole hexamer in the asymmetric unit. The active-site lid (residues 162-182) presented significant structural differences among monomers. Interestingly the region with the largest differences, when compared with the Escherichia coli homologue, was found to be close to the active site. These structural differences can be related to the kinetic and allosteric properties of both mammalian enzymes.

---

Related Citations: 

• Glucosamine-6-phosphate deaminase from beef kidney is an allosteric system of the V-type.
  Lara-Lemus, R., Calcagno, M.L.
  (1998) Biochim Biophys Acta 1388: 1

• Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 A resolution.
  Oliva, G., Fontes, M.R., Garratt, R.C., Altamirano, M.M., Calcagno, M.L., Horjales, E.
  (1995) Structure 3: 1323

---

Organizational Affiliation: 

Instituto de Biotecnología, Universidad Nacional Autónoma de México, PO Box 510-3, Cuernavaca, 62250 Morelos, Mexico. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosamine-6-phosphate isomerase	A, B, C, D, E, F	289	Homo sapiens	Mutation(s): 0  Gene Names: GNPI OR HLN OR KIAA0060, GNPDA1, GNPI, HLN, KIAA0060 EC: 3.5.99.6
Find proteins for P46926 (Homo sapiens) Explore P46926  Go to UniProtKB:  P46926
NIH Common Fund Data Resources
PHAROS:  P46926 GTEx:  ENSG00000113552

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	G, H, I, J, K, L	2		N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
16G	A, B, C, D, E, F	2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose C8 H16 N O9 P BRGMHAYQAZFZDJ-PVFLNQBWSA-N
AGP	A, B, C, D, E, F	2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE C6 H16 N O8 P LBNVXZROMBUNNQ-SLPGGIOYSA-N
SO4	A, B, C, D, E, F	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	G, H, I, J, K, L	trehalose	Oligosaccharide /  Nutrient		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.217 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.877	α = 90
b = 110.892	β = 90
c = 180.881	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-10 
• Released Date: 2003-09-23 
Deposition Author(s): Arreola, R., Valderrama, B., Morante, M.L., Horjales, E.
• This entry supersedes: 1D9T

Revision History 

• Version 1.0: 2003-09-23
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2020-10-14
  Changes: Structure summary