BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 26742

Title: Backbone and Partial Side-Chain Chemical Shift Assignments and Dynamics Measurements for The Catalytic Domain of Human Prolyl Hydroxylase Domain 2 (PHD2) With Zn(II), 2-Oxoglutarate (2OG) and Hypoxia Inducible Factor-alpha (HIF-alpha) Peptide   PubMed: 29522057

Authors: Leung, Ivanhoe; Cantrelle, Francois-Xavier; Hardy, Adam; Landrieu, Isabelle; Schofield, Christopher; Claridge, Timothy

Citation: Abboud, Martine; McAllister, Tom; Leung, Ivanhoe; Chowdhury, Rasheduzzaman; Jorgensen, Christian; Domene, Carmen; Mecinovic, Jasmin; Lippl, Kerstin; Hancock, Rebecca; Hopkinson, Richard; Kawamura, Akane; Claridge, Timothy; Schofield, Christopher. "2-Oxoglutarate regulates binding of hydroxylated hypoxia-inducible factor to prolyl hydroxylase domain 2."  Chem. Commun. (Camb.) 54, 3130-3133 (2018).

Assembly members:
PHD2, polymer, 228 residues, Formula weight is not available
entity_ZN, non-polymer, 65.409 Da.
entity_AKG, non-polymer, 146.098 Da.
CODD, polymer, 19 residues, Formula weight is not available

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
PHD2: GSHMASPNGQTKPLPALKLA LEYIVPCMNKHGICVVDDFL GKETGQQIGDEVRALHDTGK FTDGQLVSQKSDSSKDIRGD KITWIEGKEPGCETIGLLMS SMDDLIRHCNGKLGSYKING RTKAMVACYPGNGTGYVRHV DNPNGDGRCVTCIYYLNKDW DAKVSGGILRIFPEGKAQFA DIEPKFDRLLFFWSDRRNPH EVQPAYATRYAITVWYFDAD ERARAKVK
CODD: DLDLEMLAPYIPMDDDFQL

Data sets:
Data typeCount
13C chemical shifts543
15N chemical shifts170
1H chemical shifts170
T1 relaxation values163
T2 relaxation values163
heteronuclear NOE values167

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1PHD21
2ZINC ION2
3Co-substrate3
4Substrate4

Entities:

Entity 1, PHD2 228 residues - Formula weight is not available

The first six amino acids of the sequence (GSHMAS) are non-native N-terminal residues that remained from thrombin protease cleavage of poly-histidine tag. The rest of the sequence represents the catalytic domain of PHD2 (residues 181-402).

1   GLYSERHISMETALASERPROASNGLYGLN
2   THRLYSPROLEUPROALALEULYSLEUALA
3   LEUGLUTYRILEVALPROCYSMETASNLYS
4   HISGLYILECYSVALVALASPASPPHELEU
5   GLYLYSGLUTHRGLYGLNGLNILEGLYASP
6   GLUVALARGALALEUHISASPTHRGLYLYS
7   PHETHRASPGLYGLNLEUVALSERGLNLYS
8   SERASPSERSERLYSASPILEARGGLYASP
9   LYSILETHRTRPILEGLUGLYLYSGLUPRO
10   GLYCYSGLUTHRILEGLYLEULEUMETSER
11   SERMETASPASPLEUILEARGHISCYSASN
12   GLYLYSLEUGLYSERTYRLYSILEASNGLY
13   ARGTHRLYSALAMETVALALACYSTYRPRO
14   GLYASNGLYTHRGLYTYRVALARGHISVAL
15   ASPASNPROASNGLYASPGLYARGCYSVAL
16   THRCYSILETYRTYRLEUASNLYSASPTRP
17   ASPALALYSVALSERGLYGLYILELEUARG
18   ILEPHEPROGLUGLYLYSALAGLNPHEALA
19   ASPILEGLUPROLYSPHEASPARGLEULEU
20   PHEPHETRPSERASPARGARGASNPROHIS
21   GLUVALGLNPROALATYRALATHRARGTYR
22   ALAILETHRVALTRPTYRPHEASPALAASP
23   GLUARGALAARGALALYSVALLYS

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Entity 3, Co-substrate - C5 H6 O5 - 146.098 Da.

1   AKG

Entity 4, Substrate 19 residues - Formula weight is not available

1   ASPLEUASPLEUGLUMETLEUALAPROTYR
2   ILEPROMETASPASPASPPHEGLNLEU

Samples:

sample_assignment: PHD2, [U-13C; U-15N; U-2H], 0.4 mM; Zinc ion 0.6875 mM; 2-Oxoglutarate 0.9167 mM; CODD 0.8 mM; TRIS, [U-2H], 50 mM; DSS 0.0667 mM; sodium azide 0.02%

sample_t1t2noe: PHD2, [U-15N], 0.4 mM; Zinc ion 0.6 mM; 2-Oxoglutarate 0.8 mM; CODD 0.8 mM; TRIS, [U-2H], 50 mM; sodium azide 0.02%

sample_conditions_1: pH: 6.6; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_assignmentisotropicsample_conditions_1
3D HNCOsample_assignmentisotropicsample_conditions_1
3D HNCAsample_assignmentisotropicsample_conditions_1
3D HNCACBsample_assignmentisotropicsample_conditions_1
3D HNCOCACBsample_assignmentisotropicsample_conditions_1
3D HNCACOsample_assignmentisotropicsample_conditions_1
3D HNCOCAsample_assignmentisotropicsample_conditions_1
3D Heteronuclear NOEsample_t1t2noeisotropicsample_conditions_1
3D T1sample_t1t2noeisotropicsample_conditions_1
3D T2sample_t1t2noeisotropicsample_conditions_1
2D 1H-15N HSQCsample_t1t2noeisotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

Analysis, CCPN - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Bruker Avance 900 MHz

Related Database Links: