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Title :   CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH D-2-HYDROXYGLUTARATE

Authors :   R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, F. Von Delf C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann

Date :   08 Mar 16 (Deposition) - 16 Mar 16 (Release) - 16 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Oxidoreductase, Tca Intermediate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann
Crystal Structure Of Jmjc Domain Of Human Histone Demethylase Uty In Complex With D-2- Hydroxyglutarate
To Be Published
PubMed: search

Molecule 1 - HISTONE DEMETHYLASE UTY
	Chains	:	A, B
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Fragment	:	JMJC DOMAIN, RESIDUES 878-1347
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN ON THE Y CHROMOSOME, UBIQUITOUSLY-TRANSCRIBED Y CHROMOSOME TETRATRICOPEPTIDE REPEAT PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 34)

No.	Name	Count	Type	Full Name
1	2HG	2	Ligand/Ion	(2R)-2-HYDROXYPENTANEDIOIC ACID
2	EDO	28	Ligand/Ion	1,2-ETHANEDIOL
3	MN	2	Ligand/Ion	MANGANESE (II) ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 15)

No.	Name	Count	Type	Full Name
1	2HG	1	Ligand/Ion	(2R)-2-HYDROXYPENTANEDIOIC ACID
2	EDO	14	Ligand/Ion	1,2-ETHANEDIOL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 15)

No.	Name	Count	Type	Full Name
1	2HG	1	Ligand/Ion	(2R)-2-HYDROXYPENTANEDIOIC ACID
2	EDO	14	Ligand/Ion	1,2-ETHANEDIOL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (34, 34)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:1199 , CYS A:1202 , CYS A:1226 , CYS A:1229	BINDING SITE FOR RESIDUE ZN A4002
02	AC2	SOFTWARE	CYS B:1199 , CYS B:1202 , CYS B:1226 , CYS B:1229	BINDING SITE FOR RESIDUE ZN B4002
03	AC3	SOFTWARE	HIS B:1014 , GLU B:1016 , HIS B:1094 , 2HG B:2274 , HOH B:3137	BINDING SITE FOR RESIDUE MN B2273
04	AC4	SOFTWARE	HIS A:1014 , GLU A:1016 , HIS A:1094 , 2HG A:2267 , HOH A:3145	BINDING SITE FOR RESIDUE MN A2266
05	AC5	SOFTWARE	LYS A:1005 , THR A:1011 , HIS A:1014 , GLU A:1016 , SER A:1022 , ASN A:1024 , TRP A:1034 , HIS A:1094 , ALA A:1106 , MN A:2266 , EDO A:2278 , HOH A:3140 , HOH A:3145 , HOH A:3316	BINDING SITE FOR RESIDUE 2HG A2267
06	AC6	SOFTWARE	LYS B:1005 , THR B:1011 , HIS B:1014 , GLU B:1016 , SER B:1022 , ASN B:1024 , TRP B:1034 , HIS B:1094 , ALA B:1106 , MN B:2273 , EDO B:2282 , HOH B:3130 , HOH B:3131 , HOH B:3137	BINDING SITE FOR RESIDUE 2HG B2274
07	AC7	SOFTWARE	ILE B:888 , TRP B:889 , ARG B:890 , ASN B:1052 , HOH B:3308	BINDING SITE FOR RESIDUE EDO B2275
08	AC8	SOFTWARE	SER A:853 , THR A:854 , GLN A:907 , GLY A:1028 , PRO A:1029 , ASN A:1103 , EDO A:2269 , EDO A:2273 , HOH A:3039	BINDING SITE FOR RESIDUE EDO A2268
09	AC9	SOFTWARE	PRO A:1029 , TRP A:1101 , EDO A:2268 , EDO A:2275 , HOH A:3083	BINDING SITE FOR RESIDUE EDO A2269
10	BC1	SOFTWARE	ARG A:1077 , HOH A:3004 , ASN B:919 , GLU B:920	BINDING SITE FOR RESIDUE EDO A2270
11	BC2	SOFTWARE	HIS A:1188 , HIS A:1197 , TYR A:1222 , VAL A:1224	BINDING SITE FOR RESIDUE EDO A2271
12	BC3	SOFTWARE	GLY A:840 , ALA A:842 , GLY A:843 , PRO A:1082 , GLY A:1083 , ASP A:1084 , HOH A:3318	BINDING SITE FOR RESIDUE EDO A2272
13	BC4	SOFTWARE	LYS A:816 , VAL B:1044 , ASP B:1047 , PHE B:1048 , ALA B:1071 , HOH B:3309	BINDING SITE FOR RESIDUE EDO B2276
14	BC5	SOFTWARE	PHE B:911 , PRO B:1029 , TRP B:1101 , EDO B:2278 , HOH B:3085	BINDING SITE FOR RESIDUE EDO B2277
15	BC6	SOFTWARE	SER B:853 , THR B:854 , PRO B:1029 , ASN B:1103 , EDO B:2277 , EDO B:2286 , HOH B:3033	BINDING SITE FOR RESIDUE EDO B2278
16	BC7	SOFTWARE	GLY A:850 , ILE A:1027 , EDO A:2268 , HOH A:3319	BINDING SITE FOR RESIDUE EDO A2273
17	BC8	SOFTWARE	LEU B:971 , THR B:972 , ARG B:979 , VAL B:980 , VAL B:981	BINDING SITE FOR RESIDUE EDO B2279
18	BC9	SOFTWARE	HIS B:864 , ASP B:957 , ASP B:960 , LYS B:963 , HOH B:3046	BINDING SITE FOR RESIDUE EDO B2280
19	CC1	SOFTWARE	LYS B:1128 , SER B:1131 , CYS B:1202 , HOH B:3208	BINDING SITE FOR RESIDUE EDO B2281
20	CC2	SOFTWARE	GLY B:996 , GLN B:1001 , TYR B:1003 , GLU B:1016 , SER B:1022 , ALA B:1106 , TRP B:1107 , ASN B:1108 , 2HG B:2274 , HOH B:3129	BINDING SITE FOR RESIDUE EDO B2282
21	CC3	SOFTWARE	THR A:829 , CYS A:1021 , ASN A:1089 , PRO A:1111 , THR A:1113 , CYS A:1115	BINDING SITE FOR RESIDUE EDO A2274
22	CC4	SOFTWARE	PRO A:1029 , GLY A:1030 , GLY A:1100 , TRP A:1101 , EDO A:2269 , HOH A:3320	BINDING SITE FOR RESIDUE EDO A2275
23	CC5	SOFTWARE	ARG A:1081 , SER B:914 , GLU B:918	BINDING SITE FOR RESIDUE EDO B2283
24	CC6	SOFTWARE	PRO A:831 , GLU A:1039 , ASN A:1089 , ALA A:1090 , THR A:1092 , CYS A:1115 , LEU A:1119 , HOH A:3160 , HOH A:3161 , HOH A:3163	BINDING SITE FOR RESIDUE EDO A2276
25	CC7	SOFTWARE	GLU A:863 , HOH A:3046 , ASN B:1214 , GLU B:1215 , THR B:1218 , HOH B:3313	BINDING SITE FOR RESIDUE EDO B2284
26	CC8	SOFTWARE	HIS B:1225 , THR B:1233 , HOH B:3314	BINDING SITE FOR RESIDUE EDO B2285
27	CC9	SOFTWARE	SER B:853 , ILE B:1027 , GLY B:1028 , PRO B:1029 , EDO B:2278	BINDING SITE FOR RESIDUE EDO B2286
28	DC1	SOFTWARE	THR B:829 , CYS B:1021 , ASN B:1089 , PRO B:1111 , THR B:1113 , CYS B:1115 , GLN B:1116	BINDING SITE FOR RESIDUE EDO B2287
29	DC2	SOFTWARE	PRO B:1029 , GLY B:1030 , GLY B:1100 , TRP B:1101 , HOH B:3315	BINDING SITE FOR RESIDUE EDO B2288
30	DC3	SOFTWARE	GLN A:1170 , HIS A:1227 , ASP A:1228 , HOH A:3236 , HOH A:3321 , THR B:1259 , LEU B:1260	BINDING SITE FOR RESIDUE EDO A2277
31	DC4	SOFTWARE	GLY A:996 , GLN A:1001 , TYR A:1003 , ALA A:1106 , TRP A:1107 , ASN A:1108 , 2HG A:2267 , HOH A:3145	BINDING SITE FOR RESIDUE EDO A2278
32	DC5	SOFTWARE	HIS A:825 , ALA A:976 , PHE A:977 , SER A:982 , GLY A:984 , HOH A:3322	BINDING SITE FOR RESIDUE EDO A2279
33	DC6	SOFTWARE	LYS A:803 , TYR A:1041 , ASN A:1072	BINDING SITE FOR RESIDUE EDO A2280
34	DC7	SOFTWARE	ILE A:811 , PRO A:823 , LEU A:824 , HOH A:3021 , HOH A:3323	BINDING SITE FOR RESIDUE EDO A2281

(no "SS Bond" information available for 5FYM)

Asymmetric Unit

No.	Residues
1	Gly A:945	-	Pro A:946
2	Gly A:1028	-	Pro A:1029
3	Gly B:1028	-	Pro B:1029

(no "SAP(SNP)/Variant" information available for 5FYM)

(no "PROSITE Motif" information available for 5FYM)

(no "Exon" information available for 5FYM)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh....eee..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhhh..eeeeeeee....................eeeeeeehhhhhhhhhhhhhhhhhhhh........eeeeeeeee......hhhhhhhhhhhhhhhh.....hhhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5fym A  801 KDKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEKRKGPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLS 1265
                                   810       820       830       840       850       860       870       880       890       900       910       920 ||    951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261    
                                                                                                                                                   922|                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                    944

Chain B from PDB  Type:PROTEIN  Length:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhhh..eeeeeeee....................eeeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeeeee......hhhhhhhhhhhhhhhh.....................eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhheee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhhh..........eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fym B  802 DKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSSSSAENL 1272
                                   811       821       831       841       851       861       871       881       891       901       911       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      
                                                                                                                                                920|                                                                                                                                                                                                                                                                                                                                      
                                                                                                                                                 946

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(no "SCOP Domain" information available for 5FYM)

(no "CATH Domain" information available for 5FYM)

(no "Pfam Domain" information available for 5FYM)

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	Cis Peptide Bonds
		Gly A:1028 - Pro A:1029	[ RasMol ]
		Gly A:945 - Pro A:946	[ RasMol ]
		Gly B:1028 - Pro B:1029	[ RasMol ]

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	UTY_HUMAN \| O14607	:	3zli 3zpo 4uf0 5a1l 5fxv 5fxw 5fxx 5fxz 5fy0 5fy1 5fy7

5fxv	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH N05859B
5fxw	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH FUMARATE
5fxx	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH OXALOACETATE
5fxz	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH CITRATE
5fy0	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH L-MALATE
5fy1	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH N08619B
5fy4	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH SUCCINATE
5fy5	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH FUMARATE
5fy7	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH SUCCINATE
5fy8	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH D- THREO-ISOCITRATE
5fy9	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH PYRUVATE
5fyb	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC1648
5fyc	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH SUCCINATE
5fyh	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH FUMARATE
5fyi	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH PYRUVATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 34)

Sites (34, 34)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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Exons (0, 0)

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Gene Ontology (10, 10)

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