Conserved Protein Domain Family
HDAC3

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cd10005: HDAC3 
Histone deacetylase 3 (HDAC3)
HDAC3 is a Zn-dependent class I histone deacetylase that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. In order to target specific chromatin regions, HDAC3 can interact with DNA-binding proteins (transcriptional factors) either directly or after forming complexes with a number of other proteins, as observed for the SMPT/N-CoR complex which recruits human HDAC3 to specific chromatin loci and activates deacetylation. Human HDAC3 is also involved in deacetylation of non-histone substrates such as RelA, SPY and p53 factors. This protein can also down-regulate p53 function and subsequently modulate cell growth and apoptosis. This gene is therefore regarded as a potential tumor suppressor gene. HDAC3 plays a role in various physiological processes, including subcellular protein localization, cell cycle progression, cell differentiation, apoptosis and survival. HDAC3 has been found to be overexpressed in some tumors including leukemia, lung carcinoma, colon cancer and maxillary carcinoma. Thus, inhibitors precisely targeting HDAC3 (in some cases together with retinoic acid or hyperthermia) could be a therapeutic drug option.
Statistics
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PSSM-Id: 212529
Aligned: 15 rows
Threshold Bit Score: 750.381
Created: 28-Dec-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
active siteZn binding site
Feature 1:active site [active site]
Evidence:
  • Comment:Active site includes Zn binding site, lipophilic tube and foot pocket.
  • Comment:Active site consists of a long narrow tunnel (that apparently serves for substrate binding) and a cavity with Zn ion (that is important for catalysis). In this structure, the tunnel is filled by the aliphatic chain of the inhibitor.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
NP_001016883   3 KTVAYFYDPDVGNFHYGTGHPMKPHRLSLTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDYIDFLQRVSPnnmqgf- 81  western clawed ...
Q803C3         3 NRTAYFYDPDVGNFHYGAGHPMKPHRLSLTHSLVLHYGLYKKMMVFKPYKASQHDMCRFHSEDYIDFLQKVSPnnmqgf- 81  zebrafish
XP_001178366   4 KTIAYFYDADVGNFHYGPGHPMKPHRLALTHNLVLNYGLYKKMQIYRPYRATAHDMCRFHSDDYIDFLQRVTPqniqnf- 82  Strongylocentro...
Q55BW2        13 TRVCYFFDQDVGNYFYGPYHPMKPHRLCLTNNLVLNYGLHKKMHLYKARPADAEDMLKFHSEDYVDFLERVTPenine-- 90  Dictyostelium d...
AAF52023       4 RRVSYFYNADVGNFHYGAGHPMKPQRLAVTHSLVMNYGLHKKMKIYRPYKASAQDMLRFHSDEYIAYLQQVTPqniqcns 83  fruit fly
XP_002602634   5 KTVAYFFDPDVGNFHYGQGHPMKPHRLALTHSLVLHYGLYKRMQVYRPYRATVHDMCRFHSEDYIDFLQRVTPqnvqnf- 83  Florida lancelet
EFX81904       7 KVVSYFHDQDVGNFHYGPLHPMKPQRLAVTHSLVLHYGMYKKMQVYRPYRASAHDMCRFHSEDYIEFLQRVSPqniqaf- 85  common water flea
ADY43856       5 RRVCYYYHPDVGSFHYGPKHPMKPQRLAAIHSLVVNYGLHNEMLVLKPPKASAIEMERFHSKDYIDFLQRVSPktadqy- 83  pig roundworm
EDO39062       4 KRVVYFYDEDVGNFHYGPGHPMKPHRLTLTHNLVFNYGLHKKMEVYKPYRATNHDMSRFHSSDYIDFLSRVTIqnnpnl- 82  starlet sea ane...
EEC17638       9 KNVMYFWDPDVGNFHYGPGHPMKPQRLSVTHSLVLHYGLYKKMQASQLSSSNSHDMCRFHSEEYIDFLERVTPqniqtf- 87  black-legged tick
Feature 1                                                               ##       ##              
NP_001016883  82 ---tkslnAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELL 158 western clawed ...
Q803C3        82 ---tkslnTFNVGGDCPVFPGLFEFCSRYTGASLQGATQLNHKICDIAINWAGGLHHAKKFEASGFCYVNDIVISILELL 158 zebrafish
XP_001178366  83 ---tkslsHFNVGDDCPVFPGLFDFCSMYTGASLEAATKLNNNLCDIAVNWAGGLHHAKKFEASGFCYVNDIVIAILEIL 159 Strongylocentro...
Q55BW2        91 ---wkdvkRFHIGEDCPVFPGLYDYCSIYSGGSIEGALKLNHRMYDIAINWSGGLHHARKDEASGFCYVNDIVLAILELL 167 Dictyostelium d...
AAF52023      84 vaytkylaHFSVGEDCPVFDGLFDFCAMYTGASLEGAQKLNHNHSDICINWSGGLHHAKKFEASGFCYVNDIVIGILELL 163 fruit fly
XP_002602634  84 ---tkslqQFNVGDDCPVFPGLFNFCSMYTGATLEGAVKLNNNICDIAVNWAGGLHHAKKFEASGFCYVNDIVIGILELL 160 Florida lancelet
EFX81904      86 ---skclgQFNVGDDCPVFDGLFDFCSMYTGASLEGATKLNHGSTDIAINWSGGLHHAKKFEASGFCYVNDIVIAILELL 162 common water flea
ADY43856      84 ---ehlfaQFNIGEDCPVFDGIFEFCSISTGASLSGVSRLNHGLSDIAINWSGGLHHAKKREASGFCYVNDIVIGILELL 160 pig roundworm
EDO39062      83 ---sksmsDFNVGEDCPVFPGLFDFCSIYTGASLEGAVRLNQGICDIAINWAGGLHHAKKCEASGFCYVNDIVVAILELL 159 starlet sea ane...
EEC17638      88 ---tkslsHFNVGDDCPVFDGLYDFCSMYTGASLEGAVKLNNECCDIAINWSGGLHHAKKFEASGFCYVNDIVIAILELL 164 black-legged tick
Feature 1                   # #                                                                  
NP_001016883 159 KYHPRVLYVDIDIHHGDGVQEAFYLTDRVMTVSFHKYGnyFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYRHLFQP 238 western clawed ...
Q803C3       159 KYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGnyFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYRQLFQP 238 zebrafish
XP_001178366 160 KYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGnhFFPGTGDMYEVGLENGRYYSINVPLKDGIDDLMYSGLFKP 239 Strongylocentro...
Q55BW2       168 KFHARVLYIDIDVHHGDGVQEAFYLTDRVMTVSFHKFGgdFFPGTGDIDEIGAKTGKLYSVNVPLADGIDDKNYLNIFKP 247 Dictyostelium d...
AAF52023     164 KYHPRVLYIDIDVHHGDGVQEAFYLTDRVMTASFHKYGnyFFPGTGDMYEIGAESGRYYSVNVPLKEGIDDQSYFQVFKP 243 fruit fly
XP_002602634 161 KYHPRVLYVDIDIHHGDGVQEAFYLTDRVMTVSFHKYGnhFFPGTGDMYEVGAEGGKYYSLNVPLKDGIDDHNYRQLFNP 240 Florida lancelet
EFX81904     163 KYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGnyFFPGTGDMYEIGAECGRYYSVNIPLKEGIDDQSYLQVFKP 242 common water flea
ADY43856     161 KYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGnyFFPGTGDMYDIGQDSGRYYAVNVPMKEGMDDENYHSLFKP 240 pig roundworm
EDO39062     160 KYHNRVLYVDIDIHHGDGVQEAFYLTDRVMTVSFHKYGnhFFPGTGDMYEVGVDNGRLYSVNVPLRDGIDDQNYASLFKP 239 starlet sea ane...
EEC17638     165 KYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGnyFFPGTGDMYELGAESGRYYSVNVPLKEGIDDASYFQVFKP 244 black-legged tick
Feature 1                            #      #                             # #                    
NP_001016883 239 VIKQVIDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVQYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLL--VD 316 western clawed ...
Q803C3       239 VIKQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEFVKGFKIPLLVLGGGGYTVRNVARCWTFETSLL--VE 316 zebrafish
XP_001178366 240 VIQSVMEFYRPSCIVLQCGADSLGCDRLGCFSLSIKGHGECVEYVKQFNVPLLVMGGGGYTVRNVARCWTYETSLL--LN 317 Strongylocentro...
Q55BW2       248 VIQGVMDYYRPSVIVLQCGADSLRFDRLGCFNLTIKGHAECVRFVKSFNIPTLVLGGGGYTVRNVARCWTYETSVC--VD 325 Dictyostelium d...
AAF52023     244 IISAIMDFYRPTAIVLQCGADSLAGDRLGCFSLSTKGHGECVKFVKELNVPTLVVGGGGYTLRNVARCWTHETSLL--VD 321 fruit fly
XP_002602634 241 IMQQVVEFFRPTCIVLQCGADSLGCDRLGCFNLSVKGHGECVSFMKGFNLPLLVLGGGGYTVRNVARCWTHETALL--LD 318 Florida lancelet
EFX81904     243 VIQYVMEFYQPTAIVLQCGADSLANDRLGCFNLSTKGHGECVKFVKDFNVPLLVLGGGGYTLRNVARCWTYETSLL--VD 320 common water flea
ADY43856     241 IIRTVIDCFDPSAIVLQCGADSLGCDRLGCFNLSFTGHGECVDFVRSLGLPMLVVGGGGYTLRNVARCWTYETAILvgKK 320 pig roundworm
EDO39062     240 VINMVIDHYQPTCIVLQCGADSLGCDRLGCFNLSTKGHGECVRFMKTFNLPMLVLGGGGYTIRNVARCWAYETSLL--VD 317 starlet sea ane...
EEC17638     245 VIQGVMEFFQPSCIVLQCGADSLAGDRLGCFNLSIRGHGECVRFIRELGLPLLVLGGGGYTVRNVARAWTYETALL--VD 322 black-legged tick
Feature 1                                                                               
NP_001016883 317 ETISEE-LPYSEYFEYFAPDFTLHPd---vSTRIENQNSRQYLDQIRQTIFENLKMLNHAPSVQIHDVPSD 383 western clawed frog
Q803C3       317 ESISDE-LPYSEYFEYFAPDFTLHPd---vSTRIENQNSRQYLEQIRQTVFENLKMLNHAPSVQIRDVPSD 383 zebrafish
XP_001178366 318 DEISNE-LPYNDYFEYFAPDFTLHPd---tTTRIENLNTKAYIDQVRQGVHDNLKCIAHAPSVQMHDVPPD 384 Strongylocentrotus purpu...
Q55BW2       326 TEVNNE-LPYNDYIQFYSPDFQLIPdytglPFKYENANTKSYLESLRIKILENLRILQWAPSVQIQDVPPD 395 Dictyostelium discoideum
AAF52023     322 QDIEND-LPATEYYDFFAPDFTLHPe---iNSRQDNANSKQYLELIVKHVYENLKMCQHSPSVQMVQTPPD 388 fruit fly
XP_002602634 319 EEVNNE-LPYNEYFEYFSPDFTLHPd---tSTRIENCNTKGYLEQIRQTINDNLKSLSHAPSVQMHDIPPD 385 Florida lancelet
EFX81904     321 EGISNE-LPYNEYFEYFAPDFSLHPd---vVTRQENANSKQYLETITKTIHENLRMIEHAPSVMMQDVPPD 387 common water flea
ADY43856     321 DEIPDEiPNNTEYLQFFAPEFTLRPt---lAKRQENQNTKEYITAIKQEVLDHLRQIRHAPSVQMQEVPPD 388 pig roundworm
EDO39062     318 QQVSTE-IPYNDYLEYFGPDFSLHPd---iASRIENQNTKQYLDQIRQTVSENLKNLNGAPSVQMQHVPPD 384 starlet sea anemone
EEC17638     323 EPVSSE-IPYNEYFEYFAPDFTLHPe----VVTRQNANSKQYLETIVRAVSENLKCLVHAPSVQMHHVPPD 388 black-legged tick

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