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- PDB-2j9i: Lengsin is a survivor of an ancient family of class I glutamine s... -

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Entry
Database: PDB / ID: 2j9i
TitleLengsin is a survivor of an ancient family of class I glutamine synthetases in eukaryotes that has undergone evolutionary re- engineering for a tissue-specific role in the vertebrate eye lens.
ComponentsGLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
KeywordsLIGASE
Function / homology
Function and homology information


: / catalytic activity / membrane / plasma membrane / cytoplasm
Similarity search - Function
Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17 Å
AuthorsWyatt, K. / White, H.E. / Wang, L. / Bateman, O.A. / Slingsby, C. / Orlova, E.V. / Wistow, G.
CitationJournal: Structure / Year: 2006
Title: Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens.
Authors: Keith Wyatt / Helen E White / Luchun Wang / Orval A Bateman / Christine Slingsby / Elena V Orlova / Graeme Wistow /
Abstract: Lengsin is a major protein of the vertebrate eye lens. It belongs to the hitherto purely prokaryotic GS I branch of the glutamine synthetase (GS) superfamily, but has no enzyme activity. Like the ...Lengsin is a major protein of the vertebrate eye lens. It belongs to the hitherto purely prokaryotic GS I branch of the glutamine synthetase (GS) superfamily, but has no enzyme activity. Like the taxon-specific crystallins, Lengsin is the result of the recruitment of an ancient enzyme to a noncatalytic role in the vertebrate lens. Cryo-EM and modeling studies of Lengsin show a dodecamer structure with important similarities and differences with prokaryotic GS I structures. GS homology regions of Lengsin are well conserved, but the N-terminal domain shows evidence of dynamic evolutionary changes. Compared with birds and fish, most mammals have an additional exon corresponding to part of the N-terminal domain; however, in human, this is a nonfunctional pseudoexon. Genes related to Lengsin are also present in the sea urchin, suggesting that this branch of the GS I family, supplanted by GS II enzymes in vertebrates, has an ancient role in metazoans.
History
DepositionNov 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2006Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Assembly

Deposited unit
A: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
B: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
C: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
D: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
E: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
F: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
G: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
H: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
I: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
J: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
K: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1
L: GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)475,05612
Polymers475,05612
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43620 Å2
ΔGint-271.2 kcal/mol
Surface area298370 Å2
MethodPQS

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Components

#1: Protein
GLUTAMATE-AMMONIA LIGASE DOMAIN-CONTAINING PROTEIN 1 / LENGSIN / LENS GLUTAMINE SYNTHASE-LIKE


Mass: 39588.000 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8CIX8*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: LENGSIN / Type: COMPLEX
Buffer solutionName: 25 MM MALONIC ACID / pH: 6 / Details: 25 MM MALONIC ACID
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 320 nm / Nominal defocus min: 170 nm
Image recordingFilm or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UROmodel fitting
2IMAGIC3D reconstruction
CTF correctionDetails: PHASE FLIPPING
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: EXACT-FILTER BACK PROJECTION / Resolution: 17 Å / Nominal pixel size: 1.4 Å / Actual pixel size: 1.45 Å
Details: THE HOMOLOGY MODEL WAS MINIMIZED IN AMBER 8 PRIOR TO MANUAL FITTING
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Details: METHOD--URO
Atomic model buildingPDB-ID: 1F52

1f52

RefinementHighest resolution: 17 Å
Refinement stepCycle: LAST / Highest resolution: 17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33420 0 0 0 33420

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