3C0Y,2VQJ,3C10


Conserved Protein Domain Family
HDAC_classIIa
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cd11681: HDAC_classIIa 
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Histone deacetylases, class IIa
Class IIa histone deacetylases are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) to yield deacetylated histones. This subclass includes animal HDAC4, HDAC5, HDAC7, and HDCA9. Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, they have N-terminal regulatory domain with two or three conserved serine residues, phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC9 is involved in regulation of gene expression and dendritic growth in developing cortical neurons. It also plays a role in hematopoiesis. HDAC7 is involved in regulation of myocyte migration and differentiation. HDAC5 is involved in integration of chronic drug (cocaine) addiction and depression with changes in chromatin structure and gene expression. HDAC4 participates in regulation of chondrocyte hypertrophy and skeletogenesis.
Links
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Statistics
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PSSM-Id: 212544
Aligned: 16 rows
Threshold Bit Score: 670.592
Created: 16-Feb-2012
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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active siteZn binding site
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:Active center contains inhibitor and a catalytic Zn ion that coordinates side chain atoms of two aspartates and one histidine, and a water molecule.
  • Structure:2VQJ; human histone deacetylase 4 binds trifluoromethylketone inhbitor and a Zn ion; contacts at 4A.
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                                                                                      
3C0Y_A      38 FTTGLIYDSVMLKHQCSCGDnsrHPEHAGRIQSIWSRLQERGLrsqCECLRGRKASLEELQSVHSERHVLLYgTNPl--s 115  human
2VQJ_A       8 FTTGLVYDTLMLKHQCTCGSsssHPEHAGRIQSIWSRLQETGLrgkCECIRGRKATLEELQTVHSEAHTLLYgTNPl--n 85   human
EEN52898   484 FTTGVVYDPLMLKHSCSCGNnsyHPEHSGRIQSVWSRLQETGLvnrCERVRSRKATIDELKTCHSEQHVYLYgTNPl--h 561  Florida lancelet
EEC18867   484 VTTGLAYDSLMLKHQCICGDyssHPEHGGRLQSIWARLQETGLaarCERIRSRKATLEEIQSCHDEGYAFMFgTNPl--n 561  black-legged tick
EFX72406   688 TSTALAYDGLMLRHQCMCGSnsaHPEHGGRLQSIWARLQETGAvhrCLRLRSRKATAEELQSVHSDVYTMLFgTEPm--h 765  common water flea
NP_572868  820 VTTGLAYDPLMLKHSCICGDnaqHPEHSGRLQSVWARLNETDLvkrCDRLRARKATQEELQTVHTEAHAMLFgSNQcqls 899  fruit fly
EDV26715    10 QITGIAYDNIMQKHMCKCENptiHRESGGRLQSIWARLREVGIlryCEKIKTRKATTQELQTVHSEKYVSSYlDKMq--v 87   Trichoplax adhae...
CCD78021   242 FTTVLAYDLGMLAHHCTCQTdanHPENPQRLISIWQRLQQTGLaakCHHQPGRRASLIELQLVHKDVYTVLFgSNPa--s 319  Schistosoma mansoni
O17323     407 CTTGLGYDQAMVRHECCCGNnasHVENGGRIQSIWSKLIEHGHvqkCEKVTAKKASLEQLQLVHSQTYTTFFaVSPt--a 484  nematode
XP_797761  622 FTTGLAYDTLMLKHQCQCGNnqnHPEHPGRLQSIWARLHERGIvsrCERIRTRKASLEELQSCHSEGYTLFFgTSQt--h 699  purple urchin

Feature 1                                                                                     #
3C0Y_A     116 RLKLDngklag-----llaqrmFVMLPCGGVGVDTDT-IWNELHSSNAARWAAGSVTDLAFKVASrelKNGFAVVRPPGH 189  human
2VQJ_A      86 RQKLDskkllg------slasvFVRLPCGGVGVDSDT-IWNEVHSAGAARLAVGCVVELVFKVATgelKNGFAVVRPPGH 158  human
EEN52898   562 RQKQDskklag------glqksFKYLPCGGLGVDADT-IWNELHSPSALRMAAGCVIELAFKVAQgelKNGFAVVRPPGH 634  Florida lancelet
EEC18867   562 RQKLEmskle-------lpiksFVMLPCGGIGVDSDT-TWNELHTASAARMATGCVIELSFKVATgeaKNGFAMVRPPGH 633  black-legged tick
EFX72406   766 RPKVDvnrfae------lpmknFVMLPCGGIGVDSDT-TWNDIHTPSAARMAAGCVIDLAFKAAMgeiRNGFAIVRPPGH 838  common water flea
NP_572868  900 RPKLEntl-----------sasFVRLSCGGLGVDLDT-TWNEHHTATAARMAAGCVIDLALKTAKgdlRNGFAVVRPPGH 967  fruit fly
EDV26715    88 TAKTDhdelevdvtdvstndlnLIRLPCGGLGIDSET-VWDPCHTPKAARIAVGCVVDLATKVARgelRNGMAIVRPPGH 166  Trichoplax adhae...
CCD78021   320 RCRIDptll---------atvrLCRLACGGVGVDSDTaWHTAGHTAHAARLAAGCVVDLACRVMLgqcPNGFALVRPPGH 390  Schistosoma mansoni
O17323     485 CLKIDansl---------plkrFLQLPCGGIGVDSDT-YFNDASTQTAARLAAGTLIELSSQVAEgrlKNGFACIRPPGH 554  nematode
XP_797761  700 KAKLDsrklal------ipklnFTWLSCGGLGVDTDT-VWHDIQSPGAVRIAAGAVIELAFKVATgelKNGFAIVRPPGH 772  purple urchin

Feature 1      #       ##                                                            # #       
3C0Y_A     190 HADHSTAMGFCFFNSVAIACRQLQQqsk---------------------------------asKILIVDWDVHHGNGTQQ 236  human
2VQJ_A     159 HAEESTPMGFCYFNSVAVAAKLLQQrls---------------------------------vsKILIVDWDVHHGNGTQQ 205  human
EEN52898   635 HAEVDQAMGFCFFNSIAVTARLLVQrlk---------------------------------lnKVLIVDWDVHHGNGTQQ 681  Florida lancelet
EEC18867   634 HAEFKQAMGFCFFNSVAIAAKQLRQklk---------------------------------meKILVIDWDVHHGNGLQQ 680  black-legged tick
EFX72406   839 HAEAQQAMGFCFFNSVAIAAKQLRLrhk---------------------------------leRILIVDWDVHHGNGTQQ 885  common water flea
NP_572868  968 HAEANLAMGFCFFNSIAIAAKLLRQrmp--------------------------------evrRILIVDWDVHHGNGTQQ 1015 fruit fly
EDV26715   167 HAGRDTAMGSCYFNSIAITASILKQkln---------------------------------lrKVLIFDWDIHHGNGTQN 213  Trichoplax adhae...
CCD78021   391 HAEPGQAMGFCYFNSVAIAAKRAQFlgsttlgtgqssvisssattlfdqstflpytiesalkpRILIVDWDIHHGNGTQT 470  Schistosoma mansoni
O17323     555 HAEHEQAMGFCFFNNVAVAVKVLQTkypa-------------------------------qcaKIAIIDWDVHHGNGTQL 603  nematode
XP_797761  773 HAETSQAMGFCFFNSIAIAAKQLRLklk---------------------------------lnKILIIDWDVHHGNSTQK 819  purple urchin

Feature 1                                                                                      
3C0Y_A     237 TFYqdpsVLYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNVNVAWAGgldppmgDPEYLAAFRIVVMPIAREFsPDLVLV 316  human
2VQJ_A     206 AFYsdpsVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGgldppmgDAEYLAAFRTVVMPIASEFaPDVVLV 285  human
EEN52898   682 MFYedgqVLYVSLHRWDSGNFFPGTGAPDECGNGAGLGKNVNISFSGgleppmgDAEYMAAFRTVVMPIAVEFsPDLVLV 761  Florida lancelet
EEC18867   681 IFYddphVLYVSLHRHDDGNFFPGTGDPQEVGVEDGTGFNVNIAWSGtlnppmgDAEYIAAFRTIVMPIARDFdPEIVLV 760  black-legged tick
EFX72406   886 IFYedphILYISIHRHDDGHFFPGTGNPLECGSEDGIGFNVNIAWSGglnpplgDAEYLAAFRALVMPIAQDFdPEIVLV 965  common water flea
NP_572868 1016 AFYqspdILYLSIHRHDDGNFFPGTGGPTECGSGAGLGFNVNISWSGalnpplgDAEYIAAFRTVVMPIARSFnPDIVLV 1095 fruit fly
EDV26715   214 TFYedpnVLTISIHRYDKGLFFPGTGAITEVGNGSGTGFNVNVAWDSgsdvkmgDPEYLAAFRCVVLPIAKMFsPDIILV 293  Trichoplax adhae...
CCD78021   471 VFYtdptVLYISLHRHDEGGFFPGTGSPEEIGSGPGEGYTINIAWPSgiv--msDAEYLAAFRLIILPVACEFqPSIVLI 548  Schistosoma mansoni
O17323     604 SFEndpnVLYMSLHRHDKGNFFPGTGSVTEVGKNDAKGLTVNVPFSGdv---mrDPEYLAAWRTVIEPVMASFcPDFIIV 680  nematode
XP_797761  820 IFYedphVLYISLHRHDNGNFFPGTGAPDESGCGAGLGYNVNIAFHGglnppmgDAEYIAAFRSIVLPIAREFsPDVVLV 899  purple urchin

Feature 1          #                                         #                                 
3C0Y_A     317 SAGFDAAEghpaplggyHVSAKCFGYMTQQLMnl--agGAVVLALEGGHdltAICDASEACVAALLgnrvdp-------- 386  human
2VQJ_A     286 SSGFDAVEghptplggyNLSARCFGYLTKQLMgl--agGRIVLALEGGHdltAICDASEACVSALLgneldp-------- 355  human
EEN52898   762 SAGFDTAEghapqlggyKVTPKCFGHMTKQLMsv--agGRVVLALEGGYdlaAICDCSEMCVQALLgdelpp-------- 831  Florida lancelet
EEC18867   761 AAGFDAAAghppplggyQISPACFAYMTKQLMtl--akGKVVLALEGGYdlpSICDCSQECVAALLgdevsp-------- 830  black-legged tick
EFX72406   966 SAGFDAATghpsplggyQVSAACFGYMTRQLMel--agGKLVMALEGGYdlpAICDASHECVRALLgdepvp-------- 1035 common water flea
NP_572868 1096 SSGFDAATghpaplggyHVSPACFGFMTRELLql--anGKVVLALEGGYdlaAICDSAQECVRALLgdpaap-------- 1165 fruit fly
EDV26715   294 SAGFNAVAgqahenfnyRVSPACFANMTRKLIes--inSKIVLALEGGHdlpAICDASESCMRALLlsdpmp-------- 363  Trichoplax adhae...
CCD78021   549 SAGFDAAPghsanlggySVSPAAFGWMTRLLSidrianSKVVLSLEGGYdmnSLCDCTEACVRALLrsaaeinernsipi 628  Schistosoma mansoni
O17323     681 SAGFDACHghpnalggyEVTPEMFGYMTKSLLny--asGKVVLALEGGYdlkSISEAAQQCVQALIgesddag------- 751  nematode
XP_797761  900 SSGFDAANghpnplggyKVTPACFSYMTRKVMgl--anGRVVLALEGGYdltAICDASEVCAQTLLgddpsp-------- 969  purple urchin

Feature 1                                          
3C0Y_A     387 -------lseegWKQKPNLNAIRSLEAVIRVHSKYW 415  human
2VQJ_A     356 -------lpekvLQQRPNANAVRSMEKVMEIHSKYW 384  human
EEN52898   832 -------lpkeiIEQPPNKNAVTSLEETIRRQTPHW 860  Florida lancelet
EEC18867   831 -------lreeeVTRQPCGAAVQVLQRTAAIQAPHW 859  black-legged tick
EFX72406  1036 -------ireeeLARRPCQNAIDSLHKVISIQQPHW 1064 common water flea
NP_572868 1166 -------iakaeLERPPCQNAINTLQKTIAIQQTHW 1194 fruit fly
EDV26715   364 ------avsseeRNKEPNQAAVKVLEKVIQIQQEHW 393  Trichoplax adhaerens
CCD78021   629 svpdliplkqseLDRVPHPSAIQTLLKVAHLHSVYW 664  Schistosoma mansoni
O17323     752 ------rlssvaLESLPNPSAVETLQKVIAIHKSYW 781  nematode
XP_797761  970 -------lsedaINGVPNANAVECLRRTIEIQSFKE 998  purple urchin

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