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- PDB-6up9: Crystal structure of T467A variant of cytosolic fumarate hydratas... -

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Basic information

Entry
Database: PDB / ID: 6up9
TitleCrystal structure of T467A variant of cytosolic fumarate hydratase from Leishmania major in a complex with malonate
ComponentsFumarate hydratase 2
KeywordsLYASE/LYASE INHIBITOR / fumarate hydratase / fumarase / Leishmania major / inhibitor / variant T467A / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / glycosome / ciliary plasm / tricarboxylic acid cycle / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding ...fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / glycosome / ciliary plasm / tricarboxylic acid cycle / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Iron-dependent fumarate hydratase / Fe-S hydro-lyase, tartrate dehydratase alpha-type, catalytic domain / : / Fumarate hydratase (Fumerase) / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain superfamily / Fumarase C-terminus
Similarity search - Domain/homology
MALONIC ACID / IRON/SULFUR CLUSTER / Fumarate hydratase 2
Similarity search - Component
Biological speciesLeishmania major strain Friedlin (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsFeliciano, P.R. / Drennan, C.L.
Funding support Brazil, United States, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/22246-4 Brazil
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural and Biochemical Investigations of the [4Fe-4S] Cluster-Containing Fumarate Hydratase fromLeishmania major.
Authors: Feliciano, P.R. / Drennan, C.L.
History
DepositionOct 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Fumarate hydratase 2
B: Fumarate hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,38711
Polymers132,9672
Non-polymers1,4209
Water13,980776
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-118 kcal/mol
Surface area33670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.653, 84.937, 240.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 28 through 54 or (resid 55...
21(chain B and (resid 28 through 43 or (resid 44...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLUGLU(chain A and (resid 28 through 54 or (resid 55...AA28 - 5464 - 90
12LYSLYSLYSLYS(chain A and (resid 28 through 54 or (resid 55...AA5591
13ASPASPALAALA(chain A and (resid 28 through 54 or (resid 55...AA28 - 56864 - 604
14ASPASPALAALA(chain A and (resid 28 through 54 or (resid 55...AA28 - 56864 - 604
15ASPASPALAALA(chain A and (resid 28 through 54 or (resid 55...AA28 - 56864 - 604
16ASPASPALAALA(chain A and (resid 28 through 54 or (resid 55...AA28 - 56864 - 604
17ASPASPALAALA(chain A and (resid 28 through 54 or (resid 55...AA28 - 56864 - 604
21ASPASPHISHIS(chain B and (resid 28 through 43 or (resid 44...BB28 - 4364 - 79
22GLNGLNGLNGLN(chain B and (resid 28 through 43 or (resid 44...BB4480
23ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
24ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
25ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
26ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
27ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
28ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
29ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
210ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
211ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
212ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
213ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604

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Components

#1: Protein Fumarate hydratase 2 / LmFH-2


Mass: 66483.445 Da / Num. of mol.: 2 / Mutation: T467A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major strain Friedlin (eukaryote)
Strain: Friedlin / Gene: FH2, LMJF_29_1960 / Production host: Escherichia coli (E. coli) / References: UniProt: E9AE57, fumarate hydratase
#2: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 12% v/v PEG3350, 10 mM ammonium citrate tribasic, 16 mM sodium acetate trihydrate, 20 mM sodium formate, 6.4 mM ammonium tartrate dibasic, 73.2 mM malonate, 12 mM RS-Malate, 4.8 mM succinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2012
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.949→50 Å / Num. obs: 97272 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.453 / Net I/σ(I): 9.3
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 97272 / CC1/2: 0.453

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5L2R

5l2r


Resolution: 1.949→49.034 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.28
RfactorNum. reflection% reflection
Rfree0.1936 4861 5 %
Rwork0.1574 --
obs0.1592 97199 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.02 Å2 / Biso mean: 28.2292 Å2 / Biso min: 10.97 Å2
Refinement stepCycle: final / Resolution: 1.949→49.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8167 0 64 783 9014
Biso mean--27.44 37.04 -
Num. residues----1064
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3096X-RAY DIFFRACTION1.315TORSIONAL
12B3096X-RAY DIFFRACTION1.315TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.949-1.97110.34971430.2971271088
1.9711-1.99430.30761600.2738305198
1.9943-2.01860.29211610.2563305099
2.0186-2.04420.24971600.2408304598
2.0442-2.07110.28841570.2292298296
2.0711-2.09950.2551600.2207302799
2.0995-2.12950.28231630.2054310299
2.1295-2.16130.26051610.2034306799
2.1613-2.1950.22141640.1913310399
2.195-2.2310.22951610.1845307599
2.231-2.26950.23611620.1957308699
2.2695-2.31070.22531610.1758305499
2.3107-2.35520.2331630.1687308999
2.3552-2.40330.20281610.1646305899
2.4033-2.45550.19481610.161306198
2.4555-2.51260.20071590.1578300996
2.5126-2.57550.17261620.152308699
2.5755-2.64510.20631640.15263120100
2.6451-2.72290.2031620.1451309399
2.7229-2.81080.20641650.14313109100
2.8108-2.91130.19571630.14093113100
2.9113-3.02780.17711650.1377312499
3.0278-3.16560.17311620.1354308498
3.1656-3.33240.17941600.1398303296
3.3324-3.54120.14971640.125312699
3.5412-3.81450.16641670.1256316599
3.8145-4.19820.15431650.1276313799
4.1982-4.80520.14871610.1189306696
4.8052-6.05230.17431710.16163237100
6.0523-49.0340.18951730.1748327796
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)
10.44320.1070.0640.8915-0.32431.0782-0.0432-0.06990.05830.105-0.055-0.0797-0.18930.12890.10330.1929-0.011-0.05290.18710.01850.19633.917542.032997.9493
21.40060.642-0.0562.35480.46230.7157-0.08610.0728-0.0349-0.11040.0542-0.0266-0.06020.09770.03830.11530.01030.00110.15960.01870.112130.709127.470381.2776
30.4070.007-0.10191.0107-0.45380.6618-0.0640.03960.1485-0.04110.0060.0802-0.23550.03260.08230.2556-0.0287-0.06850.17760.02690.224327.938349.782279.9199
41.8290.0624-0.34891.8067-0.48892.29740.1010.04540.0547-0.175-0.02750.221-0.0731-0.2449-0.0660.3375-0.0177-0.1140.17080.05110.291219.609256.979674.0137
51.48190.04260.35042.01870.05251.41610.0383-0.3113-0.08440.2054-0.014-0.03510.0426-0.1078-0.02540.17420.00450.02840.25580.05640.138419.618420.4142113.3004
60.65920.12360.10060.67830.06971.1412-0.0158-0.0474-0.01440.0404-0.01430.14880.0561-0.2020.02140.10370.00350.00040.18160.01260.172811.55421.743593.4028
70.5443-0.07710.25760.69950.25391.91670.07480.0316-0.1286-0.1038-0.07010.11560.4433-0.25890.01820.239-0.0516-0.0290.1697-0.00660.226110.23364.962177.5683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 220 )A28 - 220
2X-RAY DIFFRACTION2chain 'A' and (resid 221 through 297 )A221 - 297
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 468 )A298 - 468
4X-RAY DIFFRACTION4chain 'A' and (resid 469 through 568 )A469 - 568
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 87 )B28 - 87
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 345 )B88 - 345
7X-RAY DIFFRACTION7chain 'B' and (resid 346 through 568 )B346 - 568

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