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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF SETD8 WITH SAM
 
Authors :  W. Yu, W. Tempel, Y. Li, M. El Bakkouri, M. Shapira, C. Bountra, C. H. Arr A. M. Edwards, P. J. Brown, Structural Genomics Consortium (Sgc)
Date :  21 Dec 12  (Deposition) - 16 Jan 13  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,I
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  I  (1x)
Keywords :  Structural Genomics Consortium, Sgc, N-Lysine Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Yu, W. Tempel, Y. Li, M. El Bakkouri, M. Shapira, C. Bountra, C. H. Arrowsmith, A. M. Edwards, P. J. Brown, Structural Genomics Consortium (Sgc)
Crystal Structure Of The Complex Of Setd8 With Sam
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - N-LYSINE METHYLTRANSFERASE SETD8
    Chains: A, B
    EC Number: 2.1.1.-, 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS2
    Expression System Strain: BL21-V2R-PRARE2
    Expression System Taxid: 511693
    Gene: SETD8, KMT5A, PRSET7, SET07, SET8
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: H4-K20-HMTASE SETD8, HISTONE-LYSINE N-METHYLTRANSFERASE SETD8, LYSINE N-METHYLTRANSFERASE 5A, PR/SET DOMAIN-CONTAINING PROTEIN 07, PR-SET7, PR/SET07, SET DOMAIN-CONTAINING PROTEIN 8
 
Molecule 2 - HELICAL PEPTIDE
    Chains: I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SEE REMARK 999
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABI
Biological Unit 1 (1x): AB 
Biological Unit 2 (1x):   I

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 34)

Asymmetric Unit (3, 34)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
2UNK10Mod. Amino Acid
3UNX22Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
2UNK-1Mod. Amino Acid
3UNX22Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SAM-1Ligand/IonS-ADENOSYLMETHIONINE
2UNK-1Mod. Amino Acid
3UNX-1Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:266 , LYS A:267 , ARG A:269 , CYS A:311 , TYR A:312 , ARG A:336 , LEU A:337 , ILE A:338 , ASN A:339 , HIS A:340 , TYR A:377 , TRP A:390 , HOH A:609 , HOH A:613 , HOH A:615 , HOH A:618 , ALA B:387BINDING SITE FOR RESIDUE SAM A 501
2AC2SOFTWAREALA A:387 , HOH A:601 , HOH A:613 , GLY B:266 , LYS B:267 , ARG B:269 , CYS B:311 , TYR B:312 , ARG B:336 , LEU B:337 , ILE B:338 , ASN B:339 , HIS B:340 , TYR B:377 , TRP B:390 , HOH B:611 , HOH B:621BINDING SITE FOR RESIDUE SAM B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IJ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IJ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IJ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IJ8)

(-) Exons   (0, 0)

(no "Exon" information available for 4IJ8)

(-) 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:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeee...eeeee.hhhhhhhhhhhhhhhh..eeeeee..eeeeee.......hhhhhee.....eeeeeeee..eeeeeeee..........ee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ij8 A 233 RKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKSGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH 393
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392 


Chain B from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh....eeeeee...eeeeee........eeee...eeeee.hhhhhhhhhhhhhhhh..eeeeee..eeeeee.......hhhhhee.....eeeeeeee..eeeeeeee..........ee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ij8 B 244 RKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKSGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH 393
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393


Chain I from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4ij8 I   4 xxxxxxxxxx  13
                            ||||||||13
                            4-UNK|||13-UNK
                             5-UNK||| 
                              6-UNK|| 
                               7-UNK| 
                                8-UNK 
                                 9-UNK
                                 10-UNK
                                  11-UNK
                                   12-UNK
   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 4IJ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IJ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IJ8)

(-) Gene Ontology  (25, 25)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KMT5A_HUMAN | Q9NQR1: 1zkk 2bqz 3f9w 3f9x 3f9y 3f9z 5hq2 5t5g 5teg 5th7 5w1y

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