2W2I | pdb_00002w2i

Crystal structure of the human 2-oxoglutarate oxygenase LOC390245

• PDB DOI: https://doi.org/10.2210/pdb2W2I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-10-31 Released: 2009-01-20 
• Deposition Author(s): Yue, W.W., Ng, S., Shafqat, N., Ugochukwu, E., McDonough, M., Pike, A.C.W., Filippakopoulos, P., von Delft, F., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Schofield, C., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.236 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Structural and Evolutionary Basis for the Dual Substrate Selectivity of Human Kdm4 Histone Demethylase Family.

Hillringhaus, L., Yue, W.W., Rose, N.R., Ng, S.S., Gileadi, C., Loenarz, C., Bello, S.H., Bray, J.E., Schofield, C.J., Oppermann, U.

(2011) J Biological Chem 286: 41616

• PubMed: 21914792 
• DOI: https://doi.org/10.1074/jbc.M111.283689
• Primary Citation Related Structures: 
  2W2I, 2XML


• PubMed Abstract: 
  

  N(ε)-Methylations of histone lysine residues play critical roles in cell biology by "marking" chromatin for transcriptional activation or repression. Lysine demethylases reverse N(ε)-methylation in a sequence- and methylation-selective manner. The determinants of sequence selectivity for histone demethylases have been unclear. The human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone. Kinetic, crystallographic, and mutagenetic studies in vitro and in cells on KDM4A-E reveal that selectivity is determined by multiple interactions within the catalytic domain but outside the active site. Structurally informed phylogenetic analyses reveal that KDM4A-C orthologues exist in all genome-sequenced vertebrates with earlier animals containing only a single KDM4 enzyme. KDM4D orthologues only exist in eutherians (placental mammals) where they are conserved, including proposed substrate sequence-determining residues. The results will be useful for the identification of inhibitors for specific histone demethylases.

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Organizational Affiliation: 
• Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.
Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom.
Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom. Electronic address: [e-mail].
Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom; Botnar Research Centre, National Institute for Health Research Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, Oxford, OX3 7LD, United Kingdom. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 124.73 kDa 
• Atom Count: 7,717 
• Modeled Residue Count: 925 
• Deposited Residue Count: 1,074 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-OXOGLUTARATE OXYGENASE	A, B, C	358	Homo sapiens	Mutation(s): 0  EC: 1.14.11 (UniProt), 1.14.11.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for B2RXH2 (Homo sapiens) Explore B2RXH2  Go to UniProtKB:  B2RXH2
PHAROS:  B2RXH2 GTEx:  ENSG00000235268

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PD2	E [auth A], I [auth B], N [auth C]	PYRIDINE-2,4-DICARBOXYLIC ACID C7 H5 N O4 MJIVRKPEXXHNJT-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	D [auth A], H [auth B], M [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PD2	BindingDB:  2W2I	Ki: 9.14e+5 (nM) from 1 assay(s)
		IC50: min: 300, max: 6310 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.236 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.904	α = 90
b = 111.009	β = 90
c = 224.199	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Yue, W.W., Ng, S., Shafqat, N., Ugochukwu, E., McDonough, M., Pike, A.C.W., Filippakopoulos, P., von Delft, F., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Schofield, C., Oppermann, U.

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2015-05-13
  Changes: Database references, Non-polymer description, Other, Refinement description, Source and taxonomy
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description