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- PDB-3p4p: Crystal structure of Menaquinol:fumarate oxidoreductase in comple... -

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Basic information

Entry
Database: PDB / ID: 3p4p
TitleCrystal structure of Menaquinol:fumarate oxidoreductase in complex with fumarate
Components(Fumarate reductase ...) x 4
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


: / fumarate reductase (quinol) / : / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration ...: / fumarate reductase (quinol) / : / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / bacterial-type flagellum assembly / tricarboxylic acid cycle / FAD binding / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA damage response / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Fumarate reductase, subunit C / Fumarate reductase subunit C / Fumarate reductase, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain ...Fumarate reductase, subunit C / Fumarate reductase subunit C / Fumarate reductase, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 3 helical TM bundles of succinate and fumarate reductases / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / Rhinovirus 14, subunit 4 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Ubiquitin-like (UB roll) / Few Secondary Structures / Irregular / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FUMARIC ACID / IRON/SULFUR CLUSTER / : / : / Fumarate reductase flavoprotein subunit / Fumarate reductase flavoprotein subunit / Fumarate reductase subunit C ...FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FUMARIC ACID / IRON/SULFUR CLUSTER / : / : / Fumarate reductase flavoprotein subunit / Fumarate reductase flavoprotein subunit / Fumarate reductase subunit C / Fumarate reductase subunit D / Fumarate reductase iron-sulfur subunit / Fumarate reductase iron-sulfur subunit
Similarity search - Component
Biological speciesEscherichia coli 042 (bacteria)
Escherichia coli 536 (bacteria)
Escherichia coli DH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsTomasiak, T.M. / Archuleta, T.L. / Andr ll, J. / Luna-Ch vez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankowskaya, V. / Stern, H.A. ...Tomasiak, T.M. / Archuleta, T.L. / Andr ll, J. / Luna-Ch vez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankowskaya, V. / Stern, H.A. / Johnston, J.N. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase.
Authors: Tomasiak, T.M. / Archuleta, T.L. / Andrell, J. / Luna-Chavez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankovskaya, V. / Stern, H.A. / Johnston, J.N. / Maklashina, E. / ...Authors: Tomasiak, T.M. / Archuleta, T.L. / Andrell, J. / Luna-Chavez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankovskaya, V. / Stern, H.A. / Johnston, J.N. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Non-polymer description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur protein
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase iron-sulfur protein
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,36817
Polymers237,0348
Non-polymers3,3349
Water1,42379
1
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur protein
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,2429
Polymers118,5174
Non-polymers1,7255
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17230 Å2
ΔGint-151 kcal/mol
Surface area39700 Å2
MethodPISA
2
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase iron-sulfur protein
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1268
Polymers118,5174
Non-polymers1,6094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17090 Å2
ΔGint-154 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.317, 137.633, 270.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Fumarate reductase ... , 4 types, 8 molecules AMBNCODP

#1: Protein Fumarate reductase flavoprotein subunit


Mass: 63477.707 Da / Num. of mol.: 2 / Fragment: UNP residues 1-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 042 (bacteria) / Strain: 042 / EAEC / Gene: frdA, EC042_4630 / Production host: Escherichia coli (E. coli)
References: UniProt: D3GV56, UniProt: P00363*PLUS, succinate dehydrogenase
#2: Protein Fumarate reductase iron-sulfur protein


Mass: 27021.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 536 (bacteria) / Strain: 536 / UPEC / Gene: ECP_4399 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0T9N6, UniProt: P0AC47*PLUS, succinate dehydrogenase
#3: Protein Fumarate reductase subunit C


Mass: 14898.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: frdC, EcDH1_3838 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QU46, UniProt: P0A8Q0*PLUS
#4: Protein Fumarate reductase subunit D


Mass: 13118.870 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: frdD, EcDH1_3839 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QU47, UniProt: P0A8Q3*PLUS

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Non-polymers , 6 types, 88 molecules

#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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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: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.8
Details: 12.5% PEG 5000 mme, 85mM MgAc, 100mM Citrate pH 5.8, 0.1% w/v DTT, 0.1mM EDTA, 5mM fumarate, vapor diffusion, temperature 298K, VAPOR DIFFUSION

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→90.76 Å / Num. obs: 84789

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→38.92 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.896 / SU B: 31.801 / SU ML: 0.298
RfactorNum. reflection% reflection
Rfree0.272 1408 1.7 %
Rwork0.249 --
obs0.249 84764 100 %
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 104.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16642 0 152 79 16873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02217423
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.97523676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15952130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34323.529748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.493152810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6515110
X-RAY DIFFRACTIONr_chiral_restr0.1990.22574
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113158
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.6091.510608
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.437217044
X-RAY DIFFRACTIONr_scbond_it7.31536815
X-RAY DIFFRACTIONr_scangle_it10.4194.56550
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å
RfactorNum. reflection% reflection
Rfree0.399 83 -
Rwork0.346 6096 -
obs--100 %
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)
10.20960.06-0.18280.12630.09270.401-0.0082-0.04380.0084-0.01360.0308-0.02550.0257-0.0237-0.02260.3809-0.00980.01380.50610.00020.48179.1129.2167-11.1191
20.20330.013-0.02830.0209-0.05180.1911-0.10610.07540.2196-0.07730.0339-0.03540.1462-0.0920.07220.3617-0.03450.05790.4135-0.04060.376713.736819.2879-36.1144
30.0952-0.0253-0.18930.18880.05160.42540.01850.04550.0659-0.1892-0.0113-0.04030.0309-0.1008-0.00720.5287-0.02740.0910.4355-0.00820.37227.174820.315-63.1735
40.2145-0.063-0.20940.14150.19040.3485-0.09780.028-0.0743-0.0388-0.01490.01390.0907-0.06290.11280.5576-0.02160.15970.363-0.01350.41633.798311.0946-65.8347
50.56331.0184-0.40221.9661-0.78850.33790.29850.09450.29410.66830.12960.6297-0.3437-0.0631-0.42810.9781-0.04760.67390.09310.00250.614213.6469-47.2521-18.6945
60.710.5268-0.26591.5084-0.88050.51840.51130.15820.10410.79-0.20640.4911-0.42810.1264-0.30490.892-0.06470.38420.1831-0.0220.452730.4994-31.5302-33.2189
70.23060.3483-0.43030.739-0.63980.81760.08360.03470.03770.1311-0.00820.0399-0.0846-0.0227-0.07530.5265-0.02380.17920.39720.00280.51345.7441-25.9245-58.39
80.18610.0231-0.15191.1277-0.1980.155-0.01770.0663-0.05390.02840.03530.22810.0103-0.0393-0.01760.5543-0.00410.19520.3439-0.00980.507643.5225-15.7689-63.5744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 576
2X-RAY DIFFRACTION2B1 - 243
3X-RAY DIFFRACTION3C1 - 130
4X-RAY DIFFRACTION4D0 - 118
5X-RAY DIFFRACTION5M0 - 576
6X-RAY DIFFRACTION6N1 - 243
7X-RAY DIFFRACTION7O1 - 130
8X-RAY DIFFRACTION8P0 - 118

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