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(-) Description

Title :  CRYSTAL STRUCTURE OF HSETD8 IN COMPLEX WITH HISTONE H4K20 NORLEUCINE MUTANT PEPTIDE AND S-ADENOSYLMETHIONINE
 
Authors :  R. A. Judge, A. M. Petros
Date :  21 Sep 16  (Deposition) - 07 Dec 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Keywords :  Transferase, Histone H4, Norleucine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. A. Judge, H. Zhu, A. K. Upadhyay, P. M. Bodelle, C. W. Hutchins, M. Torrent, V. L. Marin, W. Yu, M. Vedadi, F. Li, P. J. Brown, W. N. Pappano, C. C. Sun, A. M. Petros
Turning A Substrate Peptide Into A Potent Inhibitor For The Histone Methyltransferase Setd8
Acs Med. Chem. Lett. V. 7 1102 2016
PubMed: search  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00303

(-) Compounds

Molecule 1 - N-LYSINE METHYLTRANSFERASE KMT5A
    ChainsA, B
    EC Number2.1.1.-, 2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)-T1R
    Expression System Taxid562
    FragmentUNP RESIDUES 234-393
    GeneKMT5A, PRSET7, SET07, SET8, SETD8
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymH4-K20-HMTASE KMT5A,HISTONE-LYSINE N-METHYLTRANSFERASE KMT5A,LYSINE N-METHYLTRANSFERASE 5A,LYSINE-SPECIFIC METHYLASE 5A, PR/SET DOMAIN-CONTAINING PROTEIN 07,PR/SET07,SET DOMAIN-CONTAINING PROTEIN 8
 
Molecule 2 - HISTONE H4 MUTANT PEPTIDE WITH H4K20NORLEUCINE
    ChainsD, E
    EngineeredYES
    FragmentUNP RESIDUES 16-23
    MutationYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABDE
Biological Unit 1 (1x)A D 
Biological Unit 2 (1x) B E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NLE2Mod. Amino AcidNORLEUCINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1NLE1Mod. Amino AcidNORLEUCINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1NLE1Mod. Amino AcidNORLEUCINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:225 , LYS A:226 , ARG A:228 , CYS A:270 , TYR A:271 , ARG A:295 , LEU A:296 , ILE A:297 , ASN A:298 , HIS A:299 , TYR A:336 , TRP A:349 , HOH A:501 , HOH A:558 , HOH A:622 , HIS D:18binding site for residue SAM A 401
2AC2SOFTWAREHOH A:615 , GLY B:225 , LYS B:226 , ARG B:228 , CYS B:270 , TYR B:271 , ARG B:295 , LEU B:296 , ILE B:297 , ASN B:298 , HIS B:299 , TYR B:336 , TRP B:349 , HOH B:509 , HOH B:546 , HOH B:551 , HOH B:573 , HOH B:587 , HOH B:619 , HIS E:18binding site for residue SAM B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TEG)

(-) 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:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeeee..eeeehhhhhhhhhhhh........eeeeee..eeeeee.......hhhhhee.....eeeeeeee..eeeeeeee..........ee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5teg A 193 KSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKSGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH 352
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

Chain B from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeeee..eeeehhhhhhhhhhhhh.......eeeeee..eeeeee.......hhhhhee.....eeeeeeee..eeeeeeee..........ee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5teg B 195 KAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKSGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH 352
                                   204       214       224       234       244       254       264       274       284       294       304       314       324       334       344        

Chain D from PDB  Type:PROTEIN  Length:8
                                        
               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
                 5teg D  16 KRHRxVLR  23
                                |   
                               20-NLE

Chain E 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
                 5teg E  17 RHRxVLR  23
                               |   
                              20-NLE

   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 5TEG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (52, 56)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H4_HUMAN | P628051kx4 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 5fwe 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5kdm 5x7x
        KMT5A_HUMAN | Q9NQR11zkk 2bqz 3f9w 3f9x 3f9y 3f9z 4ij8 5hq2 5t5g 5th7 5w1y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5TEG)