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


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 

wwPDB Validation 3D Report Full Report



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

  • 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-phos ...

    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. arreola@ibt.unam.mx



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucosamine-6-phosphate isomeraseABCDEF289Homo sapiensMutation(s): 0 
Gene Names: GNPI OR HLN OR KIAA0060GNPDA1GNPIHLNKIAA0060
EC: 3.5.99.6
Find proteins for P46926 (Homo sapiens)
Explore P46926 
Go to UniProtKB:  P46926
NIH Common Fund Data Resources
PHAROS  P46926
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
G, H, I, J, K, L
2 N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
16G
Query on 16G

Download CCD File 
A, B, C, D, E, F
2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose
C8 H16 N O9 P
BRGMHAYQAZFZDJ-PVFLNQBWSA-N
 Ligand Interaction
AGP
Query on AGP

Download CCD File 
A, B, C, D, E, F
2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE
C6 H16 N O8 P
LBNVXZROMBUNNQ-SLPGGIOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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 = 109.877α = 90
b = 110.892β = 90
c = 180.881γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

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