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- PDB-2y34: S-nitrosylated PHD2 (NO exposed) in complex with Fe(II) and UN9 -

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Basic information

Entry
Database: PDB / ID: 2y34
TitleS-nitrosylated PHD2 (NO exposed) in complex with Fe(II) and UN9
ComponentsEGL NINE HOMOLOG 1
KeywordsOXIDOREDUCTASE / NON-HEME / TRANSCRIPTION AND EPIGENETIC REGULATION
Function / homology
Function and homology information


peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / peptidyl-proline dioxygenase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / regulation of modification of postsynaptic structure / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity ...peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / peptidyl-proline dioxygenase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / regulation of modification of postsynaptic structure / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation / cardiac muscle tissue morphogenesis / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / enzyme inhibitor activity / regulation of neuron apoptotic process / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to hypoxia / intracellular iron ion homeostasis / response to hypoxia / postsynaptic density / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / q2cbj1_9rhob like domain ...: / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Chem-UN9 / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsChowdhury, R. / McDonough, M.A. / Schofield, C.J.
Citation
Journal: J. Mol. Biol. / Year: 2011
Title: Studies on the reaction of nitric oxide with the hypoxia-inducible factor prolyl hydroxylase domain 2 (EGLN1).
Authors: Chowdhury, R. / Flashman, E. / Mecinovic, J. / Kramer, H.B. / Kessler, B.M. / Frapart, Y.M. / Boucher, J.L. / Clifton, I.J. / McDonough, M.A. / Schofield, C.J.
#1: Journal: Structure / Year: 2009
Title: Structural Basis for Binding of Hypoxia-Inducible Factor to the Oxygen-Sensing Prolyl Hydroxylases.
Authors: Chowdhury, R. / McDonough, M.A. / Mecinovic, J. / Loenarz, C. / Flashman, E. / Hewitson, K.S. / Domene, C. / Schofield, C.J.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Cellular Oxygen Sensing: Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (Phd2).
Authors: McDonough, M.A. / Li, V. / Flashman, E. / Chowdhury, R. / Mohr, C. / Lienard, B.M.R. / Zondlo, J. / Oldham, N.J. / Clifton, I.J. / Lewis, J. / Mcneill, L.A. / Kurzeja, R.J.M. / Hewitson, K.S. ...Authors: McDonough, M.A. / Li, V. / Flashman, E. / Chowdhury, R. / Mohr, C. / Lienard, B.M.R. / Zondlo, J. / Oldham, N.J. / Clifton, I.J. / Lewis, J. / Mcneill, L.A. / Kurzeja, R.J.M. / Hewitson, K.S. / Yang, E. / Jordan, S. / Syed, R.S. / Schofield, C.J.
History
DepositionDec 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 20, 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.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.pdbx_leaving_atom_flag / _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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EGL NINE HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7434
Polymers28,1261
Non-polymers6173
Water2,036113
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.302, 110.302, 40.378
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein EGL NINE HOMOLOG 1 / HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2 / PROLYL HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2 / SM- ...HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2 / PROLYL HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2 / SM-20 / HIF-PH2 / HIF-PROLYL HYDROXYLASE 2 / HPH-2 / PHD2


Mass: 28125.939 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 181-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3)
References: UniProt: Q9GZT9, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-UN9 / N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE


Mass: 280.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9ClN2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.32 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M AMMONIUM SULFATE, 4% DIOXANE, 0.1M MES PH6.5, VAPOR DIFFUSION, HANGING DROP, PRE-GROWN CRYSTALS WERE EXPOSED TO NITRIC OXIDE SATURATED SOLUTION (1 ML, DENSITY 1.34 G/L) FOR AN HOUR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: May 13, 2005 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.01→27.58 Å / Num. obs: 18814 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.42
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.07 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G19

2g19


Resolution: 2.01→27.58 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 108842.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TREATMENT OF PHD2 WITH GSNO RESULTED IN S-NITROSYLATION OF CYS 302, WHICH WAS REFINED AS R-S-NO. HOWEVER, THE DIHEDRAL ANGLE FOR THE C-S-N-O GROUP SUGGESTS THAT THE MODIFIED RESIDUE MAY, AT ...Details: TREATMENT OF PHD2 WITH GSNO RESULTED IN S-NITROSYLATION OF CYS 302, WHICH WAS REFINED AS R-S-NO. HOWEVER, THE DIHEDRAL ANGLE FOR THE C-S-N-O GROUP SUGGESTS THAT THE MODIFIED RESIDUE MAY, AT LEAST IN PART, BE THE R-S-N*-OH, WHICH IS A PROPOSED REACTION INTERMEDIATE OF NO WITH THIOLS, OR THE O- CENTRED THIONITROXIDE RADICAL R-S-NH-O*. OTHER POTENTIAL FORMS SUCH AS R-S-NH-OH MAY ALSO RESULT FROM PARTIAL REDUCTION OF R-S- NO DURING DATA COLLECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 986 5.6 %RANDOM
Rwork0.221 ---
obs0.221 18814 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2117 Å2 / ksol: 0.347596 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.17 Å21.47 Å20 Å2
2---3.17 Å20 Å2
3---6.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.01→27.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 39 113 1854
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 2.01→2.08 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.31 80 5.6 %
Rwork0.312 1353 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4SNC.PARSNC.TOP
X-RAY DIFFRACTION5UN9.PARUN9.TOP

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