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(-) Description

Title :  JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15) R3ME2S PEPTIDE
 
Authors :  R. Chowdhury, L. J. Walport, C. J. Schofield
Date :  15 Feb 16  (Deposition) - 06 Apr 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Jmjd2A, Oxidoreductase, Non-Heme, Iron, 2-Oxoglutarate, Dioxygenase, Oxygenase, Double-Stranded Beta Helix, Dsbh, Facial Triad, Demethylase, Histone, Jmjc Domain, Metal Binding Protein, Epigenetic And Transcription Regulation, Chromatin Regulator, Hydroxylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Walport, R. J. Hopkinson, R. Chowdhury, R. Schiller, W. Ge, A. Kawamura, C. J. Schofield
Arginine Demethylation Is Catalysed By A Subset Of Jmjc Histone Lysine Demethylases.
Nat. Commun. V. 7 11974 2016
PubMed-ID: 27337104  |  Reference-DOI: 10.1038/NCOMMS11974

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4A
    Chains: A, B
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, JUMONJI DOMAIN-CONTAINING PROTEIN 2A, JUMONJI DOMAIN CONTAINING PROTEIN 2A
 
Molecule 2 - SYNTHETIC PEPTIDE
    Chains: C, D
    Fragment: HISTONE H4(1-15)R3ME2S PEPTIDE, UNP RESIDUES 2-16
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  B D
Biological Unit 2 (1x): A C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 11)

Asymmetric Unit (6, 11)
No.NameCountTypeFull Name
12MR2Mod. Amino AcidN3, N4-DIMETHYLARGININE
2CL2Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4NI2Ligand/IonNICKEL (II) ION
5OGA2Ligand/IonN-OXALYLGLYCINE
6ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
12MR1Mod. Amino AcidN3, N4-DIMETHYLARGININE
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4NI-1Ligand/IonNICKEL (II) ION
5OGA1Ligand/IonN-OXALYLGLYCINE
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
12MR1Mod. Amino AcidN3, N4-DIMETHYLARGININE
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4NI-1Ligand/IonNICKEL (II) ION
5OGA1Ligand/IonN-OXALYLGLYCINE
6ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:188 , GLU A:190 , HIS A:276 , OGA A:1358 , HOH A:2102BINDING SITE FOR RESIDUE NI A1355
2AC2SOFTWARECYS A:234 , HIS A:240 , CYS A:306 , CYS A:308BINDING SITE FOR RESIDUE ZN A1356
3AC3SOFTWAREPHE A:227 , GLY A:229 , SER A:230BINDING SITE FOR RESIDUE CL A1357
4AC4SOFTWARETYR A:132 , PHE A:185 , HIS A:188 , GLU A:190 , SER A:196 , ASN A:198 , LYS A:206 , TRP A:208 , THR A:270 , HIS A:276 , NI A:1355 , HOH A:2102 , HOH A:2189BINDING SITE FOR RESIDUE OGA A1358
5AC5SOFTWAREHIS B:188 , GLU B:190 , HIS B:276 , OGA B:1359 , HOH B:2112BINDING SITE FOR RESIDUE NI B1356
6AC6SOFTWARECYS B:234 , HIS B:240 , CYS B:306 , CYS B:308BINDING SITE FOR RESIDUE ZN B1357
7AC7SOFTWAREPHE B:227 , PRO B:228 , GLY B:229BINDING SITE FOR RESIDUE CL B1358
8AC8SOFTWARETYR B:132 , PHE B:185 , HIS B:188 , GLU B:190 , SER B:196 , ASN B:198 , LYS B:206 , TRP B:208 , THR B:270 , HIS B:276 , NI B:1356 , HOH B:2202 , 2MR D:3BINDING SITE FOR RESIDUE OGA B1359
9AC9SOFTWARETYR B:59 , ARG B:98BINDING SITE FOR RESIDUE GOL B1360

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FWE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FWE)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  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:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee...........hhhhh..ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhh...........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhhhhhhhhhhh............hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fwe A   7 TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346        


Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh......eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee.............hhhh.ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhh..hhhhhhh............hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fwe B   3 SESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK 355
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   


Chain C from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 5fwe C   2 Gr   3
                             |
                             3-2MR


Chain D from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 5fwe D   1 SGr   3
                              |
                              |
                              3-2MR
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (53, 56)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        H4_HUMAN | P62805: 1kx4 1kx5 1m18 1m19 1m1a 1s32 1zkk 2bqz 2cv5 2ig0 2kwn 2kwo 2lvm 2qqs 2rje 2rny 2rs9 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3cfs 3cfv 3f9w 3f9x 3f9y 3f9z 3ij1 3jpx 3nqj 3nqu 3o36 3qby 3qzs 3qzt 3qzv 3r45 3uvw 3uvx 3uvy 3uw9 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4gqb 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4m38 4n3w 4n4f 4qut 4quu 4qyd 4u9w 4ym5 4ym6 4yy6 4yyd 4yyg 4yyh 4yyi 4yyj 4yyk 4yym 4yyn 4z2m 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b33 5b40 5bnv 5bnx 5bo0 5c3i 5cpi 5cpj 5cpk 5fa5 5ffw 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5kdm 5teg 5x7x
        KDM4A_HUMAN | O75164: 2gf7 2gfa 2gp3 2gp5 2oq6 2oq7 2os2 2ot7 2ox0 2p5b 2pxj 2q8c 2q8d 2q8e 2qqr 2qqs 2vd7 2wwj 2ybk 2ybp 2ybs 3njy 3pdq 3rvh 3u4s 4ai9 4bis 4gd4 4ura 4v2v 4v2w 5a7n 5a7o 5a7p 5a7q 5a7s 5a7w 5a80 5anq 5d6w 5d6x 5d6y 5f2s 5f2w 5f32 5f37 5f39 5f3c 5f3e 5f3g 5f3i 5f5i 5fpv 5fy8 5fyc 5fyh 5fyi 5ly1 5ly2 5tvr 5tvs

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