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(-) Description

Title :  CRYSTAL STRUCTURE OF DNMT3A-DNMT3L COMPLEX
 
Authors :  L. Wang, X. Guo, J. Li, J. Xiao, X. Yin, S. He, J. Wang, Y. Xu
Date :  31 Jul 14  (Deposition) - 12 Nov 14  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.82
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Methyltransferase, Autoinhibitory Form, Transferase-Transferase Regulator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Guo, L. Wang, J. Li, Z. Ding, J. Xiao, X. Yin, S. He, P. Shi, L. Dong, G. Li, C. Tian, J. Wang, Y. Cong, Y. Xu
Structural Insight Into Autoinhibition And Histone H3-Induced Activation Of Dnmt3A
Nature V. 517 640 2015
PubMed-ID: 25383530  |  Reference-DOI: 10.1038/NATURE13899

(-) Compounds

Molecule 1 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 3A
    Chains: A
    EC Number: 2.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 455-912
    Gene: DNMT3A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA METHYLTRANSFERASES DNMT3A
 
Molecule 2 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 3-LIKE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 178-379
    Gene: DNMT3L
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA METHYLTRANSFERASES DNMT3L

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2ZN3Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:537 , CYS A:540 , CYS A:559 , CYS A:562binding site for residue ZN A 1001
2AC2SOFTWARECYS A:494 , CYS A:497 , CYS A:514 , CYS A:517binding site for residue ZN A 1002
3AC3SOFTWARECYS A:549 , CYS A:554 , CYS A:583 , CYS A:586binding site for residue ZN A 1003
4AC4SOFTWAREPHE A:640 , ASP A:641 , ILE A:643 , THR A:645 , GLU A:664 , VAL A:665 , CYS A:666 , ASP A:686 , VAL A:687 , GLY A:707 , PRO A:709 , LEU A:730 , ARG A:891 , SER A:892 , TRP A:893binding site for residue SAH A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U7P)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:536 -Cys A:537
2Glu A:629 -Lys A:630
3Ser B:213 -Asp B:214
4Pro B:215 -Gly B:216

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U7P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U7P)

(-) Exons   (0, 0)

(no "Exon" information available for 4U7P)

(-) Sequences/Alignments

Asymmetric/Biological 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:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhh..........ee......eehhhhhhhhhhhhhhh.................eee........eeehhhhhhhh..hhhhhhh..............ee..ee...hhhhhhhhhh........................eeeeee....hhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh...eeee......hhhhhhhh....eeeee..hhhhh..............hhhhhhhhhhhh...........eeeeeee...hhhhhhhhhhhhh...eeee.hhh.....eeeeee.................hhhhh.....ee...........ee....ee..hhhhhhhhhh...........hhhhhhhhhhh..hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4u7p A 474 RTRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFANNHDQEFDPPKVYPPVPAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTVNDKLELQECLEHGRIAKFSKVRTQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV 912
                                   483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       846       856       866       876       886       896       906      
                                                                                                                                                                                                                                                                                                                                                                                                832|                                                                  
                                                                                                                                                                                                                                                                                                                                                                                                 846                                                                  


Chain B from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh....eeee...hhhhhhhh...........eeee.hhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhh....eeeeee....eeeeeeeee.............hhhhhhhhhhhh.......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u7p B 179 FETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSAKWPTKLVKNCFLPLREYFKYF 378
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348    || 361       371       
                                                                                                                                                                                                        353|                     
                                                                                                                                                                                                         357
   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 4U7P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U7P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U7P)

(-) Gene Ontology  (61, 67)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:629 - Lys A:630   [ RasMol ]  
    Pro B:215 - Gly B:216   [ RasMol ]  
    Ser B:213 - Asp B:214   [ RasMol ]  
    Tyr A:536 - Cys A:537   [ RasMol ]  
 

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  DNM3A_HUMAN | Q9Y6K1
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  DNM3L_HUMAN | Q9UJW3
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNM3A_HUMAN | Q9Y6K1: 2qrv 3a1a 3a1b 3llr 3svm 4qbq 4qbr 4qbs 4u7t
        DNM3L_HUMAN | Q9UJW3: 2pv0 2pvc 2qrv 4u7t

(-) Related Entries Specified in the PDB File

4u7t