Citations in PubMed

Primary Citation PubMed: 21251231 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Factor-inhibiting hypoxia-inducible factor (FIH) catalyses the post-translational hydroxylation of histidinyl residues within ankyrin repeat domains.

(2011) FEBS J 278

PubMed: 21251231 | PubMedCentral: PMC3569879 | DOI: 10.1111/j.1742-4658.2011.08022.x

Database The coordinates for the structure have been deposited in the Protein Data Bank in Europe (PDBe; ) under accession code 2y0i Structured digital abstract FIH and TNKS-... hydroxylate by enzymatic study (View Interaction 1, 2) FIH and Tankyrase-2 bind by x-ray crystallography (View interaction) FIH and Tankyrase-2 hydroxylate by enzymatic study (View Interaction 1, 2, 3) FIH and TRPV4 hydroxylate by enzymatic study (View interaction) GABPB2 and FIH hydroxylate by enzymatic study (View interaction) Factor-inhibiting hypoxia-inducible factor (FIH) is an asparaginyl hydroxylase that catalyses the β-hydroxylation of an Asn-residue in the C-terminal transcriptional activation domain of the hypoxia inducible factor and of highly conserved Asn-residues within the ubiquitous ankyrin repeat domain protein family.

(A) Surface representation of the FIH·TNKS2 538–558 dimer structure (PDB ID: 2Y0I) to 2.28 Å resolution showing apparent electron density for residues Ser 540 to His 553 of the TNKS2 538–558 peptide (2 F o − F c map, contoured to 1σ).

Publication Year: 2011

Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily.

(2013) PLoS One 8

PubMed: 24040257 | PubMedCentral: PMC3765361 | DOI: 10.1371/journal.pone.0074477

A. Mn ion of oxalate oxidase coordinated by His88, His90, Glu95, and His137 (PDB code: 2et1) [72] , B. N-terminal Mn ion of oxalate decarboxylase coordinated by His95, His97, Glu101, and His140 (PDB c... de: 1uw8) [43] , C. C-terminal Mn ion of oxalate decarboxylase coordinated by His273, His275, Glu280, and His319 (PDB code: 1uw8) [43] , D. Ni ion of cysteine dioxygenase coordinated by His86, His88, and His140 (PDB code: 2q4s) [48] , E. Zn ion of phosphomannose isommerase coordinated by Gln111, His113, Glu138, and His285 (PDB code: 1 pmi) [53] F. Ni ion of acireductone dioxygenase coordinated by His96, His98, Glu102, and His140 (PDB code: 1 zrr) [62] , G. Fe ion of taurine/alphaketoglutarate dioxygenase coordinated by His99, Asp101, and His255 (PDB code: 1os7) [73] , H. Fe ion of hypoxia-inducible factor 1-alpha inhibitor coordinated by His199, Asp201, and His279 (PBD code: 2y0i) [74] , I. Fe ion of lysine-specific demethylase 6B coordinated by His1390, Glu1392, and His1470 (PDB code: 2 xue) [75] , J. Zn ion of lysine-specific demethylase 6B coordinated by Cys1575, Cys1578, Cys1602, and Cys1605 (not part of the cupin domain) (PDB code: 2 xue) [75] .

In the more stringent sequence similarity network ( Figure 6B ), six JmjC domain-containing protein structures and the ‘cupin 8’ structures cluster together (PDB codes: 2yu2, 3k3n, 3n9l, 3pu8, 3u78, 3ld8, 4 aap, 3a16, 2y0i), while five JmjC domain-containing protein structures form an exclusive cluster (PDB codes: 2gp3, 2w2i, 2 xml, 3 dxu, 3 opt).

A. oxalate oxidase (PDB code: 2et1) [72] , B. oxalate decarboxylase (PDB code: 1uw8) [43] , C. seed storage protein Ara h (PDB code: 3s7i) [39] , D. NovW, a 4-keto-6-deoxy sugar epimerase (PDB code: 2c0z) [71] , E. cysteine dioxygenase (PDB code: 2q4s) [48] , F. phosphomannose isomerase (PDB code: 1 pmi) [53] G. acireductone dioxygenase (PDB code: 1 zrr) [62] H. taurine/alpha-ketoglutarate dioxygenase (PDB code: 1os7) [73] , I. hypoxia-inducible factor 1-alpha inhibitor (PBD code: 2y0i) [74] , J. lysine-specific demethylase 6B (PDB code: 2 xue) [75] .

Lysine-specific demethylase 6B Homo sapiens 2 xue JmjC Fe, Zn [75] JmjC domain-containing histone demethylation protein 1 a Homo sapiens 2yu2 JmjC Fe Lysine-specific demethylase 6A Homo sapiens 3 avr JmjC Ni, Zn [76] catalytic domain of PHD finger protein 8 Homo sapiens 3k3n JmjC Fe [77] Lysine-specific demethylase 7 Caenorhabditis elegans 3n9l JmjC Fe, Zn [78] PHD finger protein 2 Homo sapiens 3pu8 JmjC Fe [79] Lysine-specific demethylase 7 Homo sapiens 3u78 JmjC Ni [80] Jumonji domain-containing protein 2A Homo sapiens 2gp3 JmjC Fe, Ni [81] Lysine-specific demethylase 4E Homo sapiens 2w2i JmjC Ni JMJD2C catalytic domain Homo sapiens 2 xml JmjC Ni, Zn JmjC domain-containing histone demethylation protein 3D Homo sapiens 3 dxu JmjC Fe DNA damage-responsive transcriptional repressor RPH1 Saccharomyces cerevisiae 3 opt JmjC Ni [82] Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 Homo sapiens 3ld8 cupin 8 Fe, Hg [83] Lysine-specific demethylase 8 Homo sapiens 4 aap cupin 8 Ni JmjC domain-containing protein C2orf60 Homo sapiens 3al6 cupin 8 Ni [84] factor inhibiting HIF1 Caenorhabditis elegans 2y0i cupin 8 Fe [74] Putative asparaginyl hydroxylase Homo sapiens 1 vrb cupin 4 Fe Lysine-specific demethylase NO66 Homo sapiens 4 diq cupin 4 Ni MYC-induced nuclear antigen Homo sapiens 2 xdv cupin 4 Cd, Ni, Mn RmlC Epimerases The RmlC epimerases in Figure 3A cluster together but share edges with other protein structures.

Publication Year: 2013

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4396695

Figure 8 Variations in the Active Site Metal Coordination Chemistry of Selected Human 2-Oxoglutarate Oxygenases (A–G) Views from the active sites of (A) OGFOD1 (PDB ID: 4NHX ), (B) ter... ination and polyadenylation protein 1 (Tpa1p) (PDB ID: 4NHK , 4NHM ), (C) HIF prolyl hydroxylase (PHD2) (PDB ID: 2G1M , 3HQR ) ( McDonough et al., 2006; Chowdhury et al., 2009 ), (D) a collagen-like prolyl 4-hydroxylase enzyme from C. reinhardtii (CrP4H) (PDB ID: 2JIG , 3GZE ) ( Koski et al., 2007, 2009 ), (E) Pseudomonas aeruginosa prolyl hydroxylase domain containing protein (PPHD) (PDB ID: 4J25 , 4IW3 ) ( Scotti et al., 2014 ), (F) factor-inhibiting HIF (FIH) (PDB ID: 1H2N , 2Y0I ) ( Elkins et al., 2007; Yang et al., 2011 ), and (G) Human γ-butyrobetaine hydroxylase (BBOX) (PDB ID: 3N6W , 3O2G ) ( Tars et al., 2010 ).

Publication Year: 2015