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

PDB DOI: https://doi.org/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 ?
R-Value Free: 0.217
R-Value Work: 0.193
R-Value Observed: 0.195

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/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.

Organizational Affiliation

Instituto de Biotecnología, Universidad Nacional Autónoma de México, PO Box 510-3, Cuernavaca, 62250 Morelos, Mexico. arreola@ibt.unam.mx

Macromolecule Content

Total Structure Weight: 202.38 kDa
Atom Count: 16,013
Modelled Residue Count: 1,651
Deposited Residue Count: 1,734
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosamine-6-phosphate isomerase	A, B, C, D, E A, B, C, D, E, F	289	Homo sapiens	Mutation(s): 0 Gene Names: GNPI OR HLN OR KIAA0060 EC: 3.5.99.6
UniProt & NIH Common Fund Data Resources
Find proteins for P46926 (Homo sapiens) Explore P46926 Go to UniProtKB: P46926
PHAROS: P46926 GTEx: ENSG00000113552
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46926
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	G, H, I, J, K G, H, I, J, K, L	2		N/A	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
16G Query on 16G Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E]	CA [auth F] M [auth A] P [auth B] S [auth C] W [auth D] CA [auth F], M [auth A], P [auth B], S [auth C], W [auth D], Z [auth E]	2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose C₈ H₁₆ N O₉ P BRGMHAYQAZFZDJ-PVFLNQBWSA-N		Interactions Focus chain CA [auth F] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth E]
AGP Query on AGP Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D]	BA [auth E] EA [auth F] O [auth A] R [auth B] V [auth C] BA [auth E], EA [auth F], O [auth A], R [auth B], V [auth C], Y [auth D]	2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE C₆ H₁₆ N O₈ P LBNVXZROMBUNNQ-SLPGGIOYSA-N		Interactions Focus chain BA [auth E] Focus chain EA [auth F] Focus chain O [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth F] Focus chain O [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain Y [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D]	AA [auth E] DA [auth F] N [auth A] Q [auth B] T [auth C] AA [auth E], DA [auth F], N [auth A], Q [auth B], T [auth C], U [auth C], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006 Query on PRD_900006	G, H, I, J, K G, H, I, J, K, L	trehalose	Oligosaccharide / Nutrient		Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length ( ? )	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-09-23

Deposition Author(s):

This entry supersedes: 1D9T

Revision History (Full details and data files)

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
Version 2.2: 2023-08-16
Changes: Advisory, Data collection, Database references, Refinement description

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Deposit Data

Help and Resources

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2