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(-) Description

Title :  CRYSTAL STRUCTURE OF H142A-Y306F HDAC8 IN COMPLEX WITH A TETRAPEPTIDE SUBSTRATE
 
Authors :  C. Decroos, M. S. Lee, D. W. Christianson
Date :  23 Aug 15  (Deposition) - 03 Feb 16  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Histone Deacetylase 8, Arginase Fold, Deacetylase, Enzyme-Substrate Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Gantt, C. Decroos, M. S. Lee, L. E. Gullett, C. M. Bowman, D. W. Christianson, C. A. Fierke
General Base-General Acid Catalysis In Human Histone Deacetylase 8.
Biochemistry V. 55 820 2016
PubMed-ID: 26806311  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B01327

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 8
    Chains: A, B
    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
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HD8
 
Molecule 2 - FLUOR-DE-LYS TETRAPEPTIDE ASSAY SUBSTRATE
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric Unit (6, 16)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2ALY4Mod. Amino AcidN(6)-ACETYLLYSINE
3GOL2Ligand/IonGLYCEROL
4K4Ligand/IonPOTASSIUM ION
5MCM2Mod. Amino Acid7-AMINO-4-METHYL-CHROMEN-2-ONE
6ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2ALY2Mod. Amino AcidN(6)-ACETYLLYSINE
3GOL1Ligand/IonGLYCEROL
4K-1Ligand/IonPOTASSIUM ION
5MCM1Mod. Amino Acid7-AMINO-4-METHYL-CHROMEN-2-ONE
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2ALY2Mod. Amino AcidN(6)-ACETYLLYSINE
3GOL1Ligand/IonGLYCEROL
4K-1Ligand/IonPOTASSIUM ION
5MCM1Mod. Amino Acid7-AMINO-4-METHYL-CHROMEN-2-ONE
6ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:178 , ASP A:267 , HOH A:514binding site for residue ZN A 401
2AC2SOFTWAREASP A:176 , ASP A:178 , 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:577 , HOH A:739binding site for residue K A 403
4AC4SOFTWAREASP B:176 , ASP B:178 , SER B:199 , LEU B:200binding site for residue K B 401
5AC5SOFTWAREASP B:178 , ASP B:267 , HOH B:509binding site for residue ZN B 402
6AC6SOFTWAREPHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:582 , HOH B:726binding site for residue K B 403
7AC7SOFTWAREGLU A:330 , ALA B:188 , PHE B:189 , HOH B:513 , HOH B:572 , HOH B:760binding site for residue GOL B 404
8AC8SOFTWARELYS A:145 , GLU A:148 , HOH A:587 , HOH A:639 , HOH C:203binding site for residue GOL C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DC8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:208 -Pro A:209
2Gly A:341 -Pro A:342
3Phe B:208 -Pro B:209
4Gly B:341 -Pro B:342

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DC8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DC8)

(-) Exons   (0, 0)

(no "Exon" information available for 5DC8)

(-) 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:363
                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dc8 A  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWAHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGFNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHV 376
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   


Chain B from PDB  Type:PROTEIN  Length:363
                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dc8 B  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWAHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGFNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHV 376
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373   


Chain C from PDB  Type:PROTEIN  Length:6
                                      
               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
                 5dc8 C   1 xRHxxx   6
                            |  |||
                            1-ACE|
                               4-ALY
                                5-ALY
                                 6-MCM


Chain D from PDB  Type:PROTEIN  Length:6
                                      
               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
                 5dc8 D   1 xRHxxx   6
                            |  |||
                            |  |||
                            1-ACE|
                               4-ALY
                                5-ALY
                                 6-MCM
   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 5DC8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DC8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DC8)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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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 4qa7 4rn0 4rn1 4rn2 5bwz 5d1b 5d1c 5d1d 5dc5 5dc6 5dc7 5fcw 5ths 5tht 5thu 5thv

(-) Related Entries Specified in the PDB File

5dc5 5dc6 5dc7