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- PDB-2jio: A New Catalytic Mechanism of Periplasmic Nitrate Reductase from D... -

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Entry
Database: PDB / ID: 2jio
TitleA New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand
ComponentsPERIPLASMIC NITRATE REDUCTASE
KeywordsOXIDOREDUCTASE / NITRATE ASSIMILATION / NITROGENOUS ACCEPTOR / IRON / TRANSPORT / MOLYBDENUM / PERIPLASMIC / DISULFIDE BOND / ELECTRON TRANSPORT / IRON-SULFUR / IRON- SULFUR / METAL-BINDING / DISSIMILATORY NITRATE REDUCTASE / MOLYBDOPTERIN COFACTOR / SULFIDO LIGAND / 4FE-4S CLUSTER / ELECTRON PARAMAGNETIC RESONANCE
Function / homology
Function and homology information


nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase complex / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / molybdopterin cofactor binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity ...nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase complex / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / molybdopterin cofactor binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding / membrane
Similarity search - Function
Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / ADC-like domains / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain ...Periplasmic nitrate reductase, large subunit / Nitrate reductase NapA-like, molybdopterin-binding domain / ADC-like domains / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / N-terminal domain of TfIIb / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Single Sheet / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-MGD / MOLYBDENUM ATOM / IRON/SULFUR CLUSTER / Periplasmic nitrate reductase
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsNajmudin, S. / Gonzalez, P.J. / Trincao, J. / Coelho, C. / Mukhopadhyay, A. / Romao, C.C. / Moura, I. / Moura, J.J.G. / Brondino, C.D. / Romao, M.J.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2008
Title: Periplasmic Nitrate Reductase Revisited: A Sulfur Atom Completes the Sixth Coordination of the Catalytic Molybdenum.
Authors: Najmudin, S. / Gonzalez, P.J. / Trincao, J. / Coelho, C. / Mukhopadhyay, A. / Cerqueira, N.M.F.S.A. / Romao, C.C. / Moura, I. / Moura, J.J.G. / Brondino, C.D. / Romao, M.J.
#1: Journal: J.Biol.Inorg.Chem. / Year: 2006
Title: Epr and Redox Properties of Periplasmic Nitrate Reductase from Desulfovibrio Desulfuricans Atcc 27774
Authors: Gonzalez, P.J. / Rivas, M.G. / Brondino, C.D. / Bursakov, S.A. / Moura, I. / Moura, J.J.G.
History
DepositionJun 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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 / pdbx_struct_conn_angle / 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 / _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_label_atom_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_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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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: PERIPLASMIC NITRATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3226
Polymers80,3941
Non-polymers1,9295
Water14,592810
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.188, 106.188, 135.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PERIPLASMIC NITRATE REDUCTASE


Mass: 80393.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: P81186, nitrate reductase

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Non-polymers , 5 types, 815 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#4: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsESSENTIAL FUNCTION FOR NITRATE ASSIMILATION
Nonpolymer detailsTHE RESIDUE A 813 WAS ORIGINALLY DEPOSITED AS A ISOLATED SULFUR ATOM. AS PART OF REMEDIATION, THIS ...THE RESIDUE A 813 WAS ORIGINALLY DEPOSITED AS A ISOLATED SULFUR ATOM. AS PART OF REMEDIATION, THIS HAS BEEN CHANGED TO UNX (UNKNOWN ATOM OR LIGAND) AS THE HETEROGEN S IS NOW OBSOLETE IN THE PDB HETGROUP DICTIONARY.

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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: 2.39 Å3/Da / Density % sol: 55.01 % / Description: NONE
Crystal growpH: 6
Details: 0.1M MES, PH 6.0, 6% PEG 8000 AS PURIFIED PROTEIN ONLY

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.7712
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.2→76 Å / Num. obs: 45024 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 34.5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 27.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 35 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 3.3 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2NAP

2nap


Resolution: 2.2→92.06 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.756 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COMPARISON WITH ALL THE DDNAPA STRUCTURES SHOW THAT 74 AMINO ACID RESIDUES HAVE SHOW THE HIGHEST VARIATIONS INCLUDING THE FOLLOWING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COMPARISON WITH ALL THE DDNAPA STRUCTURES SHOW THAT 74 AMINO ACID RESIDUES HAVE SHOW THE HIGHEST VARIATIONS INCLUDING THE FOLLOWING REGIONS, RESIDUES 4-7, 27- 28, 75- 76, 94-103, 183-184, 257-259, 385-392, 505-506, 533- 534, 555-556, 575-576, 617-618, 628-640, 650-658. 675-677 AND 690-694. THESE ARE ALL ON THE PROTEIN SURFACE AND INCLUDE LOOPS AND TURNS. THE AMINO ACID SIDE CHAINS WHICH SHOW MOST FLEXIBILITY INCLUDE THE FOLLOWING, LYSINES (7, 27, 75, 259, 380, 636, 722), ARGININES (4, 544, 652), GLUTAMATES (6, 257, 287, 386, 541, 608, 647, 648) AND GLUTAMINES (193, 510). SOME OF THESE HAVE BEEN ASSIGNED WITH ALTERNATE CONFORMATIONS. SOME OF THESE DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2267 5 %RANDOM
Rwork0.15 ---
obs0.153 42713 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.15 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å2-1.15 Å20 Å2
2---2.29 Å20 Å2
3---3.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→92.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 104 810 6536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225929
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9788069
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6485719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33722.92274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86815959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0841556
X-RAY DIFFRACTIONr_chiral_restr0.1110.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024586
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.23026
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23904
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2729
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6341.53691
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01225800
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96832585
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7644.52257
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.33 166
Rwork0.238 3094
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)
11.448-0.07950.51931.3433-0.29690.8528-0.0275-0.16280.09660.23010.00960.2858-0.1631-0.15270.0179-0.03030.01840.0748-0.092-0.07550.023260.196621.989615.7176
21.2453-0.06540.51240.7524-0.03320.9098-0.00030.02-0.12320.00530.04860.20640.0272-0.0683-0.0483-0.122-0.02380.0092-0.0981-0.05350.093454.73854.76130.3724
31.037-0.12860.23870.8650.02150.6267-0.06430.1023-0.06510.05280.0046-0.0361-0.02810.09410.0597-0.0485-0.01040.0005-0.0683-0.0263-0.018889.44813.66217.6021
41.0407-0.07910.3430.8638-0.12450.6909-0.04460.26330.0333-0.1013-0.05210.0498-0.06590.14860.0967-0.0791-0.0349-0.0181-0.0554-0.0282-0.070478.796616.0182-5.5525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 61
2X-RAY DIFFRACTION1A464 - 492
3X-RAY DIFFRACTION1A517 - 561
4X-RAY DIFFRACTION2A62 - 135
5X-RAY DIFFRACTION2A347 - 463
6X-RAY DIFFRACTION2A493 - 516
7X-RAY DIFFRACTION3A136 - 346
8X-RAY DIFFRACTION4A562 - 723

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