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(-) Description

Title :  CRYSTAL STRUCTURE OF DOUBLE TUDOR DOMAIN OF HUMAN LYSINE DEMETHYLASE KDM4A COMPLEXED WITH HISTONE H3K23ME3
 
Authors :  F. Wang, Z. Su, M. D. Miller, J. M. Denu, G. N. Phillips Jr. , Enzyme Disc Natural Product Biosynthesis (Natpro)
Date :  13 Aug 15  (Deposition) - 10 Feb 16  (Release) - 07 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym. Unit :  A,B,C,D,E,F,a,b,c,d
Biol. Unit 1:  A,a  (1x)
Biol. Unit 2:  B,b  (1x)
Biol. Unit 3:  C,c  (1x)
Biol. Unit 4:  D,d  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Double Tudor Domain, Reader Domain, Structural Genomics, Psi-2, Protein Structure Initiative, Enzyme Discovery For Natural Product Biosynthesis, Natpro, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Su, F. Wang, J. H. Lee, K. E. Stephens, R. Papazyan, E. Voronina, K. A. Krautkramer, A. Raman, J. J. Thorpe, M. D. Boersma, V. I. Kuznetsov, M. D. Miller, S. D. Taverna, G. N. Phillips, J. M. Denu
Reader Domain Specificity And Lysine Demethylase-4 Family Function.
Nat Commun V. 7 13387 2016
PubMed-ID: 27841353  |  Reference-DOI: 10.1038/NCOMMS13387

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4A
    Chains: A, B, C, D, E, F
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, JUMONJI DOMAIN-CONTAINING PROTEIN 2A
 
Molecule 2 - PEPTIDE H3K23ME3 (19-28)
    Chains: a, b, c, d
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFabcd
Biological Unit 1 (1x): A     a   
Biological Unit 2 (1x):  B     b  
Biological Unit 3 (1x):   C     c 
Biological Unit 4 (1x):    D     d
Biological Unit 5 (1x):     E     
Biological Unit 6 (1x):      F    

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1M3L4Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1M3L-1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1M3L-1Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 5D6Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D6Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D6Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D6Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D6Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5D6Y)

(-) 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:108
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.....eeeeeeeeeeeeeeeeeee...eeeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeeee....eeeee...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                5d6y A  898 SITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYT 1005
                                   907       917       927       937       947       957       967       977       987       997        


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.....eeeeeeeeeeeeeeeeeee...eeeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeeee....eeeee...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                5d6y B  898 SITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYT 1005
                                   907       917       927       937       947       957       967       977       987       997        


Chain C from PDB  Type:PROTEIN  Length:104
                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....eeeeeeeeeeeeeeeeeee...eeeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeee...eeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                5d6y C  898 SITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFGSQLVVKRDDV 1003
                                   907       917       927       937       947       957       967       977       987  ||   999    
                                                                                                                      990|          
                                                                                                                       993          


Chain D from PDB  Type:PROTEIN  Length:104
                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....eeeeeeeeeeeeeeeeeee...eeeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeee...eeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                5d6y D  898 SITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFGSQLVVKRDDV 1003
                                   907       917       927       937       947       957       967       977       987  ||   999    
                                                                                                                      990|          
                                                                                                                       993          


Chain E from PDB  Type:PROTEIN  Length:107
                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.....eeeeeeeeeeeeeeeeeee....eeeeehhhhh...hhhhhh......eeee......eeeeeeeeeeeeeeeeee....eeeee...ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                5d6y E  898 SITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYT 1005
                                   907       917       927       937       947       957       968       978       988       998       
                                                                                             965|                                      
                                                                                              967                                      


Chain F from PDB  Type:PROTEIN  Length:108
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.....eeeeeeeeeeeeeeeeeee....eeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeeee...eeeeee...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                5d6y F  898 SITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYT 1005
                                   907       917       927       937       947       957       967       977       987       997        


Chain a from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .....ee.. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                5d6y a   19 QLATkAARK   27
                                |    
                               23-M3L


Chain b from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .....ee.. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                5d6y b   19 QLATkAARK   27
                                |    
                               23-M3L


Chain c from PDB  Type:PROTEIN  Length:7
                                        
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....ee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                5d6y c   20 LATkAAR   26
                               |   
                              23-M3L


Chain d from PDB  Type:PROTEIN  Length:7
                                        
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....ee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                5d6y d   20 LATkAAR   26
                               |   
                              23-M3L
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5D6Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D6Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D6Y)

(-) Gene Ontology  (50, 53)

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  KDM4A_HUMAN | O75164
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 Related Entries

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

UniProtKB/Swiss-Prot
        H31_HUMAN | P68431: 1cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
        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 5f2s 5f2w 5f32 5f37 5f39 5f3c 5f3e 5f3g 5f3i 5f5i 5fpv 5fwe 5fy8 5fyc 5fyh 5fyi 5ly1 5ly2 5tvr 5tvs

(-) Related Entries Specified in the PDB File

5d6w 5d6x