1C3R,1VKG,3MAX


Conserved Protein Domain Family
HDAC_classI

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cd09991: HDAC_classI 
Click on image for an interactive view with Cn3D
Class I histone deacetylases
Class I histone deacetylases (HDACs) are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases in general act via the formation of large multiprotein complexes. This group includes animal HDAC1, HDAC2, HDAC3, HDAC8, fungal RPD3, HOS1 and HOS2, plant HDA9, protist, archaeal and bacterial (AcuC) deacetylases. Members of this class are involved in cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and in posttranslational control of the acetyl coenzyme A synthetase. In mammals, they are known to be involved in progression of various tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs.
Statistics
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PSSM-Id: 212517
Aligned: 38 rows
Threshold Bit Score: 383.857
Created: 23-Dec-2010
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active siteZn binding site
Conserved site includes 10 residues -Click on image for an interactive view with Cn3D
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.
  • Structure:3MAX: human histone deacetylase 2 binds amino benzamide (inhibitor) and Zn ion; contacts at 4A.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                     
1C3R_A      7 IGTLDYGKyrypknhplkipRVSLLLRFKDAMnlid---ekeLIKSRPATKEELLLFHTEDYINTLMEaersqsv----- 78  Aquifex aeolicus
1VKG_A     19 IYSPEYVSmcdsl--akipkRASMVHSLIEAYalhk---qmrIVKPKVASMEEMATFHTDAYLQHLQKvsqegdd----- 88  human
CBZ27466   88 FVDHSVTAiayaeghlmrpsRVRALHALVHSLgldsa-eymtVCHARPATAEEMGAFHRSAYLECLRQapvicgnpldei 166 Leishmania mexican...
EER17726   49 DIGAFKFAvggcgdhpmdpeRLRLTHSLIESEspmn---rlsLYSFQPATFDELAVFHDRRYLEFIRNpseadrkn---- 121 Perkinsus marinus ...
EDO98539    1 YYNPELSQfslgedhpmvpnRLHLTHRLAELWglfedpnvtiVREYAPATTAQLRRFHTDEYIAFLDMtpeeqqe----- 75  Chlamydomonas rein...
EAN77596   17 CYSADCTLsalvpqhamkpyRLLVTMELIASLglkr---fcrTVVPPPIGIKELLTYHAEDYILNLGLhsnrswl----- 88  Trypanosoma brucei...
EFV62082   12 FISPYVGDhhygpghpmkpqRVAVTNSLVYQYgltk---ymdTYMAMPASDENLKEFHAPAYVDFLKQlnihnfh----- 83  Trichinella spiralis
P53096     31 HFNSKVSHyhygvkhpmkpfRLMLTDHLVSSYglhk---imdLYETRSATRDELLQFHSEDYVNFLSKvspenank---- 103 Saccharomyces cere...
EFO62784    9 FYNPLFPTfyfglhhpmkpfRIALVNELILAYglde---hlnYYTPRDATFQDMALYHTPDYIRFLKNitpetls----- 80  Giardia lamblia P15
3MAX_A      8 YYDGDIGNyyygqghpmkphRIRMTHNLLLNYglyr---kmeIYRPHKATAEEMTKYHSDEYIKFLRSirpdnms----- 79  human
Feature 1                                                                    ##       ##      
1C3R_A     79 ----pkgareKYNIgg---yENPVSyAMFTGSSLATGSTVQAIEEFlk----gnVAFNPAGGMHHAFksRANGFCYINNP 147 Aquifex aeolicus
1VKG_A     89 ----dhpdsiEYGLg----yDCPATeGIFDYAAAIGGATITAAQCLidg--mckVAINWSGGWHHAKkdEASGFCYLNDA 158 human
CBZ27466  167 slafqkefdvPFASqn---gDCPLFpEVWALVSSQAGASLACAEALvrg--datVAMNWAGGMHHAAaaHASGFCFVNDI 241 Leishmania mexican...
EER17726  122 ---havdpfvKYNLsllpwtDCTLFeGVYDYCCRTAGASLDAAQWLcdntddrpIAINWNGGMHHAHcaNAAGFCYVNDI 198 Perkinsus marinus ...
EDO98539   76 ---klgddlaMFGLsg---gDCPIFpGLLKYVGLQAAGSILAARDLasg--acdVAVHWGGGMHHGMpyRAFGFCYVNDL 147 Chlamydomonas rein...
EAN77596   89 ----wntevsKVTFs----gDCPPVeGIVEYSLSTVSGSLMAAVLLnsg--avdTAIHWGGGMHHAKcgECSGFCYVNDI 158 Trypanosoma brucei...
EFV62082   84 ---hqnqeivRSYLd----tDCPFFhGLYDYCASYAGASLAAASHLnhg--kadIAINWSGGLHHAKmsKASGFCYINDI 154 Trichinella spiralis
P53096    104 ---lprgtleNFNIg----dDCPIFqNLYDYTTLYTGASLDATRKLinn--qsdIAINWSGGLHHAKknSPSGFCYVNDI 174 Saccharomyces cere...
EFO62784   81 ---kfqdlakRYNIt----eDCPVFsGLYDYCSMTVGASVSACAHLnhg--mcdVALNWMGGFHHAKasEASGFCYANDL 151 Giardia lamblia P15
3MAX_A     80 ---eyskqmqRFNVg----eDCPVFdGLFEFCQLSTGGSVAGAVKLnrq--qtdMAVNWAGGLHHAKksEASGFCYVNDI 150 human
Feature 1                         # #                                                         
1C3R_A    148 AVGIEYLrkkgfkRILYIDLDAHHCDGVQEAFYDTdQVFVLSLHQSpeyafpfekgf-----leeigegkgkGYNLNIPL 222 Aquifex aeolicus
1VKG_A    159 VLGILRLrrk-feRILYVDLDLHHGDGVEDAFSFTsKVMTVSLHKFspgffpgtgd------vsdvglgkgrYYSVNVPI 231 human
CBZ27466  242 VLCIRRLlrh-yqRVLYVDLDVHHGDGVEGAFYGNhRVMTLSLHQFgngffpgtg--------dyptretadSFAINVPL 312 Leishmania mexican...
EER17726  199 VLAIVKLler-yeRVLYVDIDYHHGDAVEEAFYSCpRVVTLSIHSApsksntisfpgtgaiydigpegspakGHAVNLPM 277 Perkinsus marinus ...
EDO98539  148 VLAVLELmqg-cgRVLYIDIDVHHGDGVETAFKRSeKVLSISLHKWddgrmqrpvffpgtgkkndlgegqgkYYTVNVPL 226 Chlamydomonas rein...
EAN77596  159 VIAIIELlkc-hdRVLYVDLDMHHGDGVDEAFCRSrRVFTLSLHKFgesffpgtgh------prdvgigngrHYTMNLAM 231 Trypanosoma brucei...
EFV62082  155 VLAILELlky-ypRVLYVDIDVHHGDGVQEAFIQSdRVLTFSSHQFsegffpgtgl------pdeigigpgkYFAVNIPL 227 Trichinella spiralis
P53096    175 VLSILNLlry-hpRILYIDIDLHHGDGVQEAFYTTdRVFTLSFHKYngeffpgtgd------lteigcdkgkHFALNVPL 247 Saccharomyces cere...
EFO62784  152 VLGILELlkv-heRVLYVDIDIHAGDGVEEAFYTTnRVLTLSFHKYdtdffpgtgn------lfdngadqgkGYAINFPL 224 Giardia lamblia P15
3MAX_A    151 VLAILELlky-hqRVLYIDIDIHHGDGVEEAFYTTdRVMTVSFHKYgeyfpgtgdl-------rdigagkgkYYAVNFPM 222 human
Feature 1                                        #      #                                     
1C3R_A    223 PKglnDNEFLFALEKSLEIVkevfePEVYLLQLGTDPLLEDYLs---kFNLSNVAFLKAFNIVRevf------------g 287 Aquifex aeolicus
1VKG_A    232 QDgiqDEKYYQICESVLKEVyqafnPKAVVLQLGADTIAGDPMc---sFNMTPVGIGKCLKYILqwq------------l 296 human
CBZ27466  313 PTrtgDAAYLLSFRTALSSVvqcfdPEAMVVQCGADTIAGDLIg---rLCVTTLAHTQCVADVLsle------------r 377 Leishmania mexican...
EER17726  278 KPglsDDMFLYALRTTLSTLvqrfrPSCLVVQSGSDSLAGDLLtshsgFNLSTRGHATAVQELRrlg------------i 345 Perkinsus marinus ...
EDO98539  227 QDdiqDDSYYAVYSSVVKAAfekfkPQAVVLQCGCDSVAGDKLg---rFNLSIRGHARCGRAGGcesgpgagrggadwri 303 Chlamydomonas rein...
EAN77596  232 WDgvdDFYYTTVFERALRSIvkrfnPNVVVLQCGADSLAGDRLg---hFNLSSWGHGKCVEEVKklg------------l 296 Trypanosoma brucei...
EFV62082  228 KEgatLATFEQAVKPLLRLAvesflPSVIVLQCGADSLACDRLg---hFSLGIEDHGVCVSFVRdfn------------l 292 Trichinella spiralis
P53096    248 EDgidDDSYINLFKSIVDPLimtfkPTLIVQQCGADSLGHDRLg---cFNLNIKAHGECVKFVKsfg------------l 312 Saccharomyces cere...
EFO62784  225 KDaidDDTFIYIFGSVVKDVmccydPQAVVLQCGADSLAGDRLg---vFNVTLKGHGECVKILYqytqa--------kgi 293 Giardia lamblia P15
3MAX_A    223 RDgidDESYGQIFKPIISKVmemyqPSAVVLQCGADSLSGDRLg---cFNLTVKGHAKCVEVVKtfn------------l 287 human
Feature 1            # #                
1C3R_A    288 eGVYLGGGGYhpyALARAWTLIWCEL 313 Aquifex aeolicus
1VKG_A    297 aTLILGGGGYnlaNTARCWTYLTGVI 322 human
CBZ27466  378 pTVLLGGGGYhvfHTARCWAIHTATA 403 Leishmania mexicana MHOM/GT/2001/U1103
EER17726  346 pTLVLGGGGYsltSVAKCWSMETAVW 371 Perkinsus marinus ATCC 50983
EDO98539  304 pLLVTGGGGYtppLVARCWALETAVL 329 Chlamydomonas reinhardtii
EAN77596  297 pMLVVGGGGYtlrNVAKLWAYETSIL 322 Trypanosoma brucei brucei strain 927/4 GUTat10.1
EFV62082  293 pMLVVGGGGYtlkNVARCWAYETSLL 318 Trichinella spiralis
P53096    313 pMLVVGGGGYtprNVSRLWTYETGIL 338 Saccharomyces cerevisiae S288c
EFO62784  294 pLLLTGGGGYtarSAAKCWTYETSLV 319 Giardia lamblia P15
3MAX_A    288 pLLMLGGGGYtirNVARCWTYETAVA 313 human

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