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(-) Description

Title :  CRYSTAL STRUCTURE OF H334R/Y306F HDAC8 IN COMPLEX WITH A TETRAPEPTIDE SUBSTRATE
 
Authors :  C. Decroos, C. B. Bowman, J. -A. S. Moser, K. E. Christianson, M. A. Deard D. W. Christianson
Date :  02 May 14  (Deposition) - 06 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metalloenzyme, Hydrolase, Histone Deacetylase, Enzyme Substrate Complex, Cornelia De Lange Syndrome, Arginase/Deacetylase Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Decroos, C. M. Bowman, J. A. Moser, K. E. Christianson, M. A. Deardorff, D. W. Christianson
Compromised Structure And Function Of Hdac8 Mutants Identified In Cornelia De Lange Syndrome Spectrum Disorders
Acs Chem. Biol. V. 9 2157 2014
PubMed-ID: 25075551  |  Reference-DOI: 10.1021/CB5003762

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 8
    Chains: A
    EC Number: 3.5.1.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHD2-XA-HIS
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HDAC8, HDACL1, CDA07
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HD8
 
Molecule 2 - TETRAPEPTIDE SUBSTRATE
    Chains: B
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2ALY2Mod. Amino AcidN(6)-ACETYLLYSINE
3GOL1Ligand/IonGLYCEROL
4K2Ligand/IonPOTASSIUM ION
5MCM1Ligand/Ion7-AMINO-4-METHYL-CHROMEN-2-ONE
6ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:178 , HIS A:180 , ASP A:267 , HOH A:522 , ALY B:505BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200BINDING SITE FOR RESIDUE K A 402
3AC3SOFTWAREPHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:523 , HOH A:536BINDING SITE FOR RESIDUE K A 403
4AC4SOFTWARELYS A:33 , TYR A:100 , ASP A:101 , PHE A:152 , PRO A:273 , ALY B:505BINDING SITE FOR RESIDUE MCM B 601
5AC5SOFTWARELYS A:145 , GLU A:148 , PHE A:208 , ARG B:502 , HIS B:503 , HOH B:702BINDING SITE FOR RESIDUE GOL B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QA7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:208 -Pro A:209
2Gly A:341 -Pro A:342

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QA7)

(-) Exons   (0, 0)

(no "Exon" information available for 4QA7)

(-) 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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhh.....hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee.......................eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qa7 A  13 SLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGFNLANTARCWTYLTGVILGKTLSSEIPDREFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    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       362       372     


Chain B from PDB  Type:PROTEIN  Length:5
                                     
               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
                 4qa7 B 501 xRHkk 505
                            |  ||
                          501-ACE
                             504-ALY
                              505-ALY
   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 4QA7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QA7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QA7)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:341 - Pro A:342   [ RasMol ]  
    Phe A:208 - Pro A:209   [ RasMol ]  
 

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  4qa7
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  3.5.1.98
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 Related Entries

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

UniProtKB/Swiss-Prot
        HDAC8_HUMAN | Q9BY41: 1t64 1t67 1t69 1vkg 1w22 2v5w 2v5x 3ew8 3ewf 3ezp 3ezt 3f06 3f07 3f0r 3mz3 3mz4 3mz6 3mz7 3rqd 3sff 3sfh 4qa0 4qa1 4qa2 4qa3 4qa4 4qa5 4qa6 4rn0 4rn1 4rn2 5bwz 5d1b 5d1c 5d1d 5dc5 5dc6 5dc7 5dc8 5fcw 5ths 5tht 5thu 5thv

(-) Related Entries Specified in the PDB File

4qa0 4qa1 4qa2 4qa3 4qa4 4qa5 4qa6