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- PDB-7ebe: Crystal structure of Isocitrate lyase-1 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 7ebe
TitleCrystal structure of Isocitrate lyase-1 from Candida albicans
ComponentsIsocitrate lyase
KeywordsLYASE / Isocitrate lyase / glyoxylate cycle / ubiquitination
Function / homology
Function and homology information


methylisocitrate lyase activity / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / peroxisome / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #850 / Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / Isocitrate lyase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsHiragi, K. / Nishio, K. / Moriyama, S. / Hamaguchi, T. / Mizoguchi, A. / Yonekura, K. / Tani, K. / Mizushima, T.
CitationJournal: J Struct Biol / Year: 2021
Title: Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.
Authors: Keito Hiragi / Kazuya Nishio / Shu Moriyama / Tasuku Hamaguchi / Akira Mizoguchi / Koji Yonekura / Kazutoshi Tani / Tsunehiro Mizushima /
Abstract: In Saccharomyces cerevisiae, the glyoxylate cycle is controlled through the posttranslational regulation of its component enzymes, such as isocitrate lyase (ICL), which catalyzes the first unique ...In Saccharomyces cerevisiae, the glyoxylate cycle is controlled through the posttranslational regulation of its component enzymes, such as isocitrate lyase (ICL), which catalyzes the first unique step of the cycle. The ICL of S.cerevisiae (ScIcl1) is tagged for proteasomal degradation through ubiquitination by a multisubunit ubiquitin ligase (the glucose-induced degradation-deficient (GID) complex), whereas that of the pathogenic yeast Candida albicans (CaIcl1) escapes this process. However, the reason for the ubiquitin targeting specificity of the GID complex for ScIcl1 and not for CaIcl1 is unclear. To gain some insight into this, in this study, the crystal structures of apo ScIcl1 and CaIcl1 in complex with formate and the cryogenic electron microscopy structure of apo CaIcl1 were determined at a resolution of 2.3, 2.7, and 2.6 Å, respectively. A comparison of the various structures suggests that the orientation of N-terminal helix α1 in S.cerevisiae is likely key to repositioning of ubiquitination sites and contributes to the distinction found in C. albicans ubiquitin evasion mechanism. This finding gives us a better understanding of the molecular mechanism of ubiquitin-dependent ScIcl1 degradation and could serve as a theoretical basis for the research and development of anti-C. albicans drugs based on the concept of CaIcl1 ubiquitination.
History
DepositionMar 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate lyase
B: Isocitrate lyase
C: Isocitrate lyase
D: Isocitrate lyase
E: Isocitrate lyase
F: Isocitrate lyase
G: Isocitrate lyase
H: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,43928
Polymers498,6928
Non-polymers74720
Water5,368298
1
A: Isocitrate lyase
B: Isocitrate lyase
C: Isocitrate lyase
D: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,81216
Polymers249,3464
Non-polymers46512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39180 Å2
ΔGint-247 kcal/mol
Surface area70710 Å2
MethodPISA
2
E: Isocitrate lyase
F: Isocitrate lyase
G: Isocitrate lyase
H: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,62712
Polymers249,3464
Non-polymers2818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37470 Å2
ΔGint-243 kcal/mol
Surface area71020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.971, 139.910, 200.301
Angle α, β, γ (deg.)90.00, 92.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLUGLUAA2 - 5408 - 546
21PROPROGLUGLUBB2 - 5408 - 546
12PROPROLYSLYSAA2 - 5448 - 550
22PROPROLYSLYSCC2 - 5448 - 550
13PROPROLYSLYSAA2 - 5448 - 550
23PROPROLYSLYSDD2 - 5448 - 550
14PROPROLYSLYSAA2 - 5448 - 550
24PROPROLYSLYSEE2 - 5448 - 550
15PROPROPHEPHEAA2 - 5438 - 549
25PROPROPHEPHEFF2 - 5438 - 549
16THRTHRPHEPHEAA4 - 54310 - 549
26THRTHRPHEPHEGG4 - 54310 - 549
17THRTHRGLNGLNAA4 - 53610 - 542
27THRTHRGLNGLNHH4 - 53610 - 542
18PROPROASPASPBB2 - 5418 - 547
28PROPROASPASPCC2 - 5418 - 547
19PROPROGLUGLUBB2 - 5408 - 546
29PROPROGLUGLUDD2 - 5408 - 546
110PROPROGLUGLUBB2 - 5408 - 546
210PROPROGLUGLUEE2 - 5408 - 546
111PROPROGLUGLUBB2 - 5408 - 546
211PROPROGLUGLUFF2 - 5408 - 546
112THRTHRASPASPBB4 - 54110 - 547
212THRTHRASPASPGG4 - 54110 - 547
113THRTHRGLNGLNBB4 - 53610 - 542
213THRTHRGLNGLNHH4 - 53610 - 542
114PROPROLYSLYSCC2 - 5448 - 550
214PROPROLYSLYSDD2 - 5448 - 550
115PROPROLYSLYSCC2 - 5448 - 550
215PROPROLYSLYSEE2 - 5448 - 550
116PROPROLYSLYSCC2 - 5448 - 550
216PROPROLYSLYSFF2 - 5448 - 550
117THRTHRPHEPHECC4 - 54310 - 549
217THRTHRPHEPHEGG4 - 54310 - 549
118THRTHRGLYGLYCC4 - 53710 - 543
218THRTHRGLYGLYHH4 - 53710 - 543
119PROPROLYSLYSDD2 - 5448 - 550
219PROPROLYSLYSEE2 - 5448 - 550
120PROPROLYSLYSDD2 - 5448 - 550
220PROPROLYSLYSFF2 - 5448 - 550
121THRTHRPHEPHEDD4 - 54310 - 549
221THRTHRPHEPHEGG4 - 54310 - 549
122THRTHRGLNGLNDD4 - 53610 - 542
222THRTHRGLNGLNHH4 - 53610 - 542
123PROPROLYSLYSEE2 - 5448 - 550
223PROPROLYSLYSFF2 - 5448 - 550
124THRTHRPHEPHEEE4 - 54310 - 549
224THRTHRPHEPHEGG4 - 54310 - 549
125THRTHRGLNGLNEE4 - 53610 - 542
225THRTHRGLNGLNHH4 - 53610 - 542
126THRTHRPHEPHEFF4 - 54310 - 549
226THRTHRPHEPHEGG4 - 54310 - 549
127THRTHRGLNGLNFF4 - 53610 - 542
227THRTHRGLNGLNHH4 - 53610 - 542
128THRTHRGLYGLYGG4 - 53710 - 543
228THRTHRGLYGLYHH4 - 53710 - 543

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Isocitrate lyase


Mass: 62336.523 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59RB8, isocitrate lyase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 22%(w/v)PEG 3350, 0.2M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.69→200.1 Å / Num. obs: 122958 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0693 / Rpim(I) all: 0.0387 / Rrim(I) all: 0.0732 / Net I/σ(I): 13.5
Reflection shellResolution: 2.69→2.79 Å / Rmerge(I) obs: 0.595 / Num. unique obs: 12109 / CC1/2: 0.849 / Rpim(I) all: 0.366 / Rrim(I) all: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EBC

7ebc


Resolution: 2.69→47.11 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 19.114 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24797 6148 5 %RANDOM
Rwork0.21468 ---
obs0.21634 116812 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.02 Å2
2---0.02 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.69→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33985 0 44 298 34327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01934795
X-RAY DIFFRACTIONr_bond_other_d0.0010.0233047
X-RAY DIFFRACTIONr_angle_refined_deg0.3981.94347048
X-RAY DIFFRACTIONr_angle_other_deg0.473376238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.70554300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58824.5621576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.754156068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.82915160
X-RAY DIFFRACTIONr_chiral_restr0.0360.25087
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0239327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027913
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.74424.48717239
X-RAY DIFFRACTIONr_mcbond_other3.74424.48717240
X-RAY DIFFRACTIONr_mcangle_it5.45127.53921526
X-RAY DIFFRACTIONr_mcangle_other5.45127.53921527
X-RAY DIFFRACTIONr_scbond_it3.89824.99517556
X-RAY DIFFRACTIONr_scbond_other3.89824.99617553
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.64827.83825523
X-RAY DIFFRACTIONr_long_range_B_refined7.2439.78541163
X-RAY DIFFRACTIONr_long_range_B_other7.2439.79941120
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A637180.09
12B637180.09
21A632700.09
22C632700.09
31A645860.08
32D645860.08
41A626900.1
42E626900.1
51A631120.1
52F631120.1
61A631160.09
62G631160.09
71A630440.1
72H630440.1
81B620940.1
82C620940.1
91B631880.09
92D631880.09
101B625600.1
102E625600.1
111B630080.1
112F630080.1
121B628040.1
122G628040.1
131B626940.1
132H626940.1
141C635880.09
142D635880.09
151C617820.1
152E617820.1
161C620520.1
162F620520.1
171C627260.09
172G627260.09
181C621360.1
182H621360.1
191D626840.11
192E626840.11
201D624760.11
202F624760.11
211D626140.1
212G626140.1
221D632160.09
222H632160.09
231E618820.11
232F618820.11
241E619420.1
242G619420.1
251E612280.11
252H612280.11
261F622440.11
262G622440.11
271F616160.11
272H616160.11
281G622040.1
282H622040.1
LS refinement shellResolution: 2.691→2.761 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 443 -
Rwork0.396 8420 -
obs--97.93 %

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