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- PDB-5zka: Crystal structure of N-acetylneuraminate lyase from Fusobacterium... -

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Basic information

Entry
Database: PDB / ID: 5zka
TitleCrystal structure of N-acetylneuraminate lyase from Fusobacterium nucleatum complexed with Pyruvate
Components(N-acetylneuraminate lyase) x 2
KeywordsLYASE / N-acetylneuraminate lyase / Sialic acid catabolism / TIM-barrel / Schiff base
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / 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
TRIETHYLENE GLYCOL / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsKumar, J.P. / Rao, H. / Nayak, V. / Ramaswamy, S.
Funding support India, 4items
OrganizationGrant numberCountry
BT/IN/SWEDEN/41/SR/2013 India
BT/PR5081/INF/156/2012 India
BT/PR12422/MED/31/287/214 India
BT/INF/22/SP22660/2017 India
Citation
Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structures and kinetics of N-acetylneuraminate lyase from Fusobacterium nucleatum
Authors: Kumar, J.P. / Rao, H. / Nayak, V. / Ramaswamy, S.
#1: Journal: Biochemistry / Year: 2013
Title: Structural basis for substrate specificity and mechanism of N-acetyl-D-neuraminic acid lyase from Pasteurella multocida.
Authors: Huynh, N. / Aye, A. / Li, Y. / Yu, H. / Cao, H. / Tiwari, V.K. / Shin, D.W. / Chen, X. / Fisher, A.J.
History
DepositionMar 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylneuraminate lyase
B: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9838
Polymers68,5222
Non-polymers4616
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-6 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.676, 86.568, 89.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein N-acetylneuraminate lyase / / Neu5Ac lyase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate ...Neu5Ac lyase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / Sialic acid aldolase / Sialic acid lyase


Mass: 34983.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Pyruvate covalently bound through a Schiff base to Lys161
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Strain: ATCC 25586 / Gene: nanA / Plasmid: pET300/NT-DEST / Details (production host): From Invitrogen / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RDN6, N-acetylneuraminate lyase
#2: Protein N-acetylneuraminate lyase / / Neu5Ac lyase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate ...Neu5Ac lyase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / Sialic acid aldolase / Sialic acid lyase


Mass: 33538.824 Da / Num. of mol.: 1 / Fragment: UNP residues 1-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Strain: ATCC 25586 / Gene: nanA / Plasmid: pET300/NT-DEST / Details (production host): From Invitrogen / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RDN6, N-acetylneuraminate lyase
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLYS 161 is modified to KPI in subunit A.

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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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1M CHES, pH 9.5 , 10% w/v PEG 3000 and 2.85 mM Sodium pyruvate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.76→86.57 Å / Num. obs: 63236 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.034 / Rrim(I) all: 0.064 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.76-1.793.40.84735480.6470.520.99998.2
8.97-86.572.90.035340.9970.020.03694.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IMC

4imc


Resolution: 1.76→60.882 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 2028 3.21 %
Rwork0.1865 61155 -
obs0.1875 63183 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.21 Å2 / Biso mean: 38.6715 Å2 / Biso min: 20.59 Å2
Refinement stepCycle: final / Resolution: 1.76→60.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4615 0 30 166 4811
Biso mean--60.89 39.22 -
Num. residues----586
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.76-1.8040.37691470.32584313446098
1.804-1.85280.36391250.29544280440597
1.8528-1.90730.3071450.25614310445598
1.9073-1.96890.28151530.22894365451898
1.9689-2.03930.25281520.21724355450799
2.0393-2.12090.22911440.214372451698
2.1209-2.21750.24611380.20054308444697
2.2175-2.33440.23351510.19344326447798
2.3344-2.48070.25271410.19634388452998
2.4807-2.67220.24031560.19474394455098
2.6722-2.94110.251370.21064369450697
2.9411-3.36660.22851500.19574422457298
3.3666-4.24150.17781430.16494397454097
4.2415-60.9180.1611460.14734556470296
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3084-0.45930.32520.88970.30091.04580.0012-0.2409-0.03780.16850.01590.00380.0662-0.0564-0.01870.2588-0.02850.02280.25970.05090.23327.932332.332641.2824
21.7683-0.75390.23810.8653-0.00961.2495-0.03860.42040.1037-0.0822-0.0679-0.0538-0.09850.08640.09720.2222-0.0663-0.01950.31910.00590.229329.74828.28773.6539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid -2 through 289)A-2 - 289
2X-RAY DIFFRACTION2(chain 'B' and resid -6 through 289)B-6 - 289

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