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- PDB-1hl2: Crystal structure of N-acetylneuraminate lyase from E. coli mutan... -

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Basic information

Entry
Database: PDB / ID: 1hl2
TitleCrystal structure of N-acetylneuraminate lyase from E. coli mutant L142R in complex with b-hydroxypyruvate
ComponentsN-ACETYLNEURAMINATE LYASE SUBUNIT
KeywordsLYASE / N-ACETYLNEURAMINATE LYASE / CLASS I ALDOLASE / CARBOHYDRATE METABOLISM / SCHIFF BASE
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / single-species biofilm formation / carbohydrate metabolic process / identical protein binding / cytosol
Similarity search - Function
N-acetylneuraminate lyase / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...N-acetylneuraminate lyase / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-HYDROXYPYRUVIC ACID / N-acetylneuraminate lyase / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJoerger, A.C. / Fersht, A.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Mimicking Natural Evolution in Vitro: An N-Acetylneuraminate Lyase Mutant with an Increased Dihydrodipicolinate Synthase Activity
Authors: Joerger, A.C. / Mayer, S. / Fersht, A.R.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: Structure and Mechanism of a Sub-Family of Enzymes Related to N-Acetylneuraminate Lyase
Authors: Lawrence, M.C. / Barbosa, J.A. / Smith, B.J. / Hall, N.E. / Pilling, P.A. / Ooi, H.C. / Marcuccio, S.M.
#2: Journal: Structure / Year: 1994
Title: The Three-Dimensional Structure of N-Acetylneuraminate Lyase from Escherichia Coli
Authors: Izard, T. / Lawrence, M.C. / Malby, R. / Lilley, G.G. / Colman, P.M.
History
DepositionMar 12, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACETYLNEURAMINATE LYASE SUBUNIT
B: N-ACETYLNEURAMINATE LYASE SUBUNIT
C: N-ACETYLNEURAMINATE LYASE SUBUNIT
D: N-ACETYLNEURAMINATE LYASE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0988
Polymers130,6824
Non-polymers4164
Water14,988832
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.740, 95.990, 89.650
Angle α, β, γ (deg.)90.00, 115.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-ACETYLNEURAMINATE LYASE SUBUNIT / N-ACETYLNEURAMINIC ACID ALDOLASE / N-ACETYLNEURAMINATE PYRUVATE LYASE / NALASE


Mass: 32670.410 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AT997
References: UniProt: P06995, UniProt: P0A6L4*PLUS, N-acetylneuraminate lyase
#2: Chemical
ChemComp-3PY / 3-HYDROXYPYRUVIC ACID


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYSES THE CONVERION OF N-ACETYLNEURAMINATE TO N-ACETYL-D-MANNOSAMINE AND PYRUVATE. ENGINEERED ...CATALYSES THE CONVERION OF N-ACETYLNEURAMINATE TO N-ACETYL-D-MANNOSAMINE AND PYRUVATE. ENGINEERED MUTATION LEU 141 ARG, CHAINS A, B, C AND D
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
220 mMBHP1drop
320 mMTris1droppH7.6
4100 mMsodium acetate1reservoirpH4.6
58 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorDate: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→37.4 Å / Num. obs: 117329 / % possible obs: 98.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 5.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.4 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 412908
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.3

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Processing

Software
NameVersionClassification
CNS1refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FDY

1fdy


Resolution: 1.8→37.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1164 -RANDOM
Rwork0.183 ---
obs0.183 117329 98.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9113 0 24 832 9969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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