2VQV - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF HDAC4 CATALYTIC DOMAIN WITH A GAIN-OF-FUNCTION MUTATION BOUND TO A HYDROXAMIC ACID INHIBITOR

Authors :   M. J. Bottomley, P. Lo Surdo, P. Di Giovine, A. Cirillo, R. Scarpelli, F. Ferrigno, P. Jones, P. Neddermann, R. De Francesco, C. Steinkuhler, P. Gallinari, A. Carfi

Date :   19 Mar 08 (Deposition) - 22 Jul 08 (Release) - 10 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Inhibitor, Repressor, Chromatin, Coiled Coil, Histone Deacetylase, Transcription Regulation, Ubl Conjugation, Chromatin Regulator, Polymorphism, Transcription, Phosphoprotein, Hdac, Zinc, Hdaci, Nucleus, Hydrolase, Cytoplasm (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Bottomley, P. Lo Surdo, P. Di Giovine, A. Cirillo, R. Scarpelli, F. Ferrigno, P. Jones, P. Neddermann, R. De Francesco, C. Steinkuhler, P. Gallinari, A. Carfi
Structural And Functional Analysis Of The Human Hdac4 Catalytic Domain Reveals A Regulatory Structural Zinc-Binding Domain.
J. Biol. Chem. V. 283 26694 2008
PubMed-ID: 18614528 | Reference-DOI: 10.1074/JBC.M803514200

Molecule 1 - HISTONE DEACETYLASE 4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM-11 (OBTAINED FROM EMBL- HEIDELBERG)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 648-1057
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HD4

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	HA3	2	Ligand/Ion	N-HYDROXY-5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHENE-2-CARBOXAMIDE
2	K	4	Ligand/Ion	POTASSIUM ION
3	SO4	4	Ligand/Ion	SULFATE ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HA3	1	Ligand/Ion	N-HYDROXY-5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHENE-2-CARBOXAMIDE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	HA3	1	Ligand/Ion	N-HYDROXY-5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHENE-2-CARBOXAMIDE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	SO4	3	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:367	BINDING SITE FOR RESIDUE SO4 A1406
02	AC2	SOFTWARE	SER B:72 , GLU B:73	BINDING SITE FOR RESIDUE SO4 B1406
03	AC3	SOFTWARE	PRO B:256 , ASN B:366 , ALA B:367	BINDING SITE FOR RESIDUE SO4 B1407
04	AC4	SOFTWARE	LYS B:20 , ARG B:37 , ARG B:154	BINDING SITE FOR RESIDUE SO4 B1408
05	AC5	SOFTWARE	ASP A:194 , ASP A:196 , HIS A:198 , SER A:217 , LEU A:218	BINDING SITE FOR RESIDUE K A1407
06	AC6	SOFTWARE	PHE A:207 , ASP A:210 , VAL A:213 , PHE A:244	BINDING SITE FOR RESIDUE K A1408
07	AC7	SOFTWARE	ASP B:194 , ASP B:196 , HIS B:198 , SER B:217 , LEU B:218	BINDING SITE FOR RESIDUE K B1409
08	AC8	SOFTWARE	PHE B:207 , ASP B:210 , VAL B:213 , PHE B:244	BINDING SITE FOR RESIDUE K B1410
09	AC9	SOFTWARE	PRO A:156 , HIS A:159 , GLY A:167 , PHE A:168 , HIS A:198 , PHE A:227 , ASP A:290 , GLY A:330 , TYR A:332 , ZN A:1410 , LEU B:78 , TYR B:79 , THR B:81 , ALA B:124	BINDING SITE FOR RESIDUE HA3 A1409
10	BC1	SOFTWARE	LEU A:78 , TYR A:79 , THR A:81 , ALA A:124 , PRO B:156 , HIS B:159 , GLY B:167 , PHE B:168 , HIS B:198 , PHE B:227 , ASP B:290 , TYR B:332 , ZN B:1412	BINDING SITE FOR RESIDUE HA3 B1411
11	BC2	SOFTWARE	ASP A:196 , HIS A:198 , ASP A:290 , HA3 A:1409	BINDING SITE FOR RESIDUE ZN A1410
12	BC3	SOFTWARE	ASP B:196 , HIS B:198 , ASP B:290 , HA3 B:1411	BINDING SITE FOR RESIDUE ZN B1412

(no "SS Bond" information available for 2VQV)

Asymmetric Unit

No.	Residues
1	Arg A:154	-	Pro A:155
2	Phe A:227	-	Pro A:228
3	Asp A:255	-	Pro A:256
4	Arg B:154	-	Pro B:155
5	Phe B:227	-	Pro B:228
6	Asp B:255	-	Pro B:256

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036042	P	727	R	HDAC4_HUMAN	Unclassified	---	A/B	P	83	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036042	P	727	R	HDAC4_HUMAN	Unclassified	---	A	P	83	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036042	P	727	R	HDAC4_HUMAN	Unclassified	---	B	P	83	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2VQV)

Asymmetric Unit (12, 24)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3	ENST00000345617	3	ENSE00001242645	chr2:240322643-240322071	573	HDAC4_HUMAN	-	0	0	-	-
1.4	ENST00000345617	4	ENSE00002161358	chr2:240274613-240274373	241	HDAC4_HUMAN	1-8	8	0	-	-
1.7b	ENST00000345617	7b	ENSE00001679522	chr2:240158360-240158289	72	HDAC4_HUMAN	8-32	25	0	-	-
1.9a	ENST00000345617	9a	ENSE00001308711	chr2:240111773-240111529	245	HDAC4_HUMAN	32-113	82	0	-	-
1.11b	ENST00000345617	11b	ENSE00001753193	chr2:240098259-240098109	151	HDAC4_HUMAN	114-164	51	0	-	-
1.12b	ENST00000345617	12b	ENSE00001708242	chr2:240085619-240085499	121	HDAC4_HUMAN	164-204	41	0	-	-
1.13	ENST00000345617	13	ENSE00001658039	chr2:240078469-240078348	122	HDAC4_HUMAN	204-245	42	0	-	-
1.15	ENST00000345617	15	ENSE00001780577	chr2:240066410-240066279	132	HDAC4_HUMAN	245-289	45	0	-	-
1.17	ENST00000345617	17	ENSE00001723920	chr2:240061492-240061380	113	HDAC4_HUMAN	289-326	38	0	-	-
1.18	ENST00000345617	18	ENSE00001752779	chr2:240056339-240056223	117	HDAC4_HUMAN	327-365	39	0	-	-
1.19b	ENST00000345617	19b	ENSE00001593963	chr2:240056139-240055941	199	HDAC4_HUMAN	366-432	67	0	-	-
1.20c	ENST00000345617	20c	ENSE00000787258	chr2:240048375-240048152	224	HDAC4_HUMAN	432-506	75	0	-	-
1.21	ENST00000345617	21	ENSE00001607824	chr2:240037006-240036749	258	HDAC4_HUMAN	507-592	86	0	-	-
1.22	ENST00000345617	22	ENSE00001621125	chr2:240033408-240033222	187	HDAC4_HUMAN	593-655	63	2	A:7-11 B:7-11	5 5
1.23a	ENST00000345617	23a	ENSE00001779179	chr2:240029879-240029746	134	HDAC4_HUMAN	655-699	45	2	A:11-55 (gaps) B:11-55 (gaps)	45 45
1.24a	ENST00000345617	24a	ENSE00001735120	chr2:240024592-240024472	121	HDAC4_HUMAN	700-740	41	2	A:56-83 B:56-84	28 29
1.25a	ENST00000345617	25a	ENSE00001623395	chr2:240016752-240016706	47	HDAC4_HUMAN	740-755	16	0	-	-
1.27a	ENST00000345617	27a	ENSE00001710463	chr2:240011812-240011705	108	HDAC4_HUMAN	756-791	36	2	A:115-147 B:115-147	33 33
1.28	ENST00000345617	28	ENSE00001659227	chr2:240009310-240009255	56	HDAC4_HUMAN	792-810	19	2	A:148-166 B:148-166	19 19
1.29	ENST00000345617	29	ENSE00001595029	chr2:240005938-240005851	88	HDAC4_HUMAN	810-839	30	2	A:166-195 B:166-195	30 30
1.30	ENST00000345617	30	ENSE00001598022	chr2:240003917-240003798	120	HDAC4_HUMAN	840-879	40	2	A:196-235 B:196-235	40 40
1.31a	ENST00000345617	31a	ENSE00001725968	chr2:240002888-240002791	98	HDAC4_HUMAN	880-912	33	2	A:236-268 B:236-268	33 33
1.32	ENST00000345617	32	ENSE00001643358	chr2:239990303-239990185	119	HDAC4_HUMAN	912-952	41	2	A:268-308 B:268-308	41 41
1.33b	ENST00000345617	33b	ENSE00001679613	chr2:239988551-239988418	134	HDAC4_HUMAN	952-996	45	2	A:308-352 B:308-352	45 45
1.35	ENST00000345617	35	ENSE00001784017	chr2:239976529-239976445	85	HDAC4_HUMAN	997-1025	29	2	A:353-381 B:353-381	29 29
1.36	ENST00000345617	36	ENSE00001770463	chr2:239975297-239975156	142	HDAC4_HUMAN	1025-1072	48	2	A:381-405 B:381-405	25 25
1.37c	ENST00000345617	37c	ENSE00001207161	chr2:239974832-239969864	4969	HDAC4_HUMAN	1072-1084	13	0	-	-

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:355
 aligned with HDAC4_HUMAN | P56524 from UniProtKB/Swiss-Prot  Length:1084

    Alignment length:399
                                   660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040         
         HDAC4_HUMAN    651 RFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCE 1049
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhh.-------------..hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhh..-------------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....................hhhhhhhhhhhhhhh...ee........hhhhhhhh.......eeeeee.................hhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeee.................hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhh..hhhhhh.......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.22 --------------------------------------------Exon 1.24a  PDB: A:56-83 UniProt: 700-740---------------Exon 1.27a  PDB: A:115-147          Exon 1.28          -----------------------------Exon 1.30  PDB: A:196-235               Exon 1.31a  PDB: A:236-268       ---------------------------------------Exon 1.33b  PDB: A:308-352 UniProt: 952-996  Exon 1.35  PDB: A:353-381    ------------------------ Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.23a  PDB: A:11-55 (gaps)              ----------------------------------------Exon 1.25a      ------------------------------------------------------Exon 1.29  PDB: A:166-195     ------------------------------------------------------------------------Exon 1.32  PDB: A:268-308                ------------------------------------------------------------------------Exon 1.36  PDB: A:381-405 Transcript 1 (2)
                2vqv A    7 RFTTGLVYDTLMLK-------------HAGRIQSIWSRLQETGLRGKCEAIRGRKATLEELQTVHSEAHTLLYGTNP-------------------------------DTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCE  405
                                    16   |     -       |36        46        56        66        76      |  -         -         -       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396         
                                        20            34                                               83                             115

Chain B from PDB  Type:PROTEIN  Length:356
 aligned with HDAC4_HUMAN | P56524 from UniProtKB/Swiss-Prot  Length:1084

    Alignment length:399
                                   660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040         
         HDAC4_HUMAN    651 RFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCE 1049
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------H             ist_deacetyl-2vqvB03 B:20-349                                                                                                                                                                                                                                                                                               ------Arb2-2vqvB01 B:356-405                             Pfam domains (1)
           Pfam domains (2) -------------H             ist_deacetyl-2vqvB04 B:20-349                                                                                                                                                                                                                                                                                               ------Arb2-2vqvB02 B:356-405                             Pfam domains (2)
         Sec.struct. author ....eee.hhhhh.-------------..hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhh...------------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....................hhhhhhhhhhhhhhh...eeeee.....hhhhhhhh.....eeeeeeee.................hhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeee.................hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhh..hhhhhh.......hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.22 --------------------------------------------Exon 1.24a  PDB: B:56-84 UniProt: 700-740---------------Exon 1.27a  PDB: B:115-147          Exon 1.28          -----------------------------Exon 1.30  PDB: B:196-235               Exon 1.31a  PDB: B:236-268       ---------------------------------------Exon 1.33b  PDB: B:308-352 UniProt: 952-996  Exon 1.35  PDB: B:353-381    ------------------------ Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.23a  PDB: B:11-55 (gaps)              ----------------------------------------Exon 1.25a      ------------------------------------------------------Exon 1.29  PDB: B:166-195     ------------------------------------------------------------------------Exon 1.32  PDB: B:268-308                ------------------------------------------------------------------------Exon 1.36  PDB: B:381-405 Transcript 1 (2)
                2vqv B    7 RFTTGLVYDTLMLK-------------HAGRIQSIWSRLQETGLRGKCEAIRGRKATLEELQTVHSEAHTLLYGTNPL------------------------------DTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCE  405
                                    16   |     -       |36        46        56        66        76       | -         -         -       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396         
                                        20            34                                                84                            115

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 '\|'

(no "SCOP Domain" information available for 2VQV)

(no "CATH Domain" information available for 2VQV)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AB_hydrolase (347)

Family: Arb2 (5)

Homo sapiens (Human) (5)

1a	Arb2-2vqvB01	B:356-405
1b	Arb2-2vqvB02	B:356-405

Clan: Arginase (56)

Family: Hist_deacetyl (19)

Homo sapiens (Human) (15)

2a	Hist_deacetyl-2vqvB03	B:20-349
2b	Hist_deacetyl-2vqvB04	B:20-349

Asymmetric Unit(hide GO term definitions)

Chain A,B (HDAC4_HUMAN | P56524)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0032041	NAD-dependent histone deacetylase activity (H3-K14 specific)	Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein.
	GO:0001025	RNA polymerase III transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase III transcription factor, any protein required to initiate or regulate transcription by RNA polymerase III.
	GO:0033613	activating transcription factor binding	Interacting selectively and non-covalently with an activating transcription factor, any protein whose activity is required to initiate or upregulate transcription.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0001047	core promoter binding	Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0004407	histone deacetylase activity	Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030955	potassium ion binding	Interacting selectively and non-covalently with potassium (K+) ions.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0033558	protein deacetylase activity	Catalysis of the hydrolysis of an acetyl group or groups from a protein substrate.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0070491	repressing transcription factor binding	Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0042113	B cell activation	The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0014898	cardiac muscle hypertrophy in response to stress	The physiological enlargement or overgrowth of all or part of the heart muscle due to an increase in size (not length) of individual cardiac muscle fibers, without cell division, as a result of a disturbance in organismal or cellular homeostasis.
	GO:0071260	cellular response to mechanical stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
	GO:0071374	cellular response to parathyroid hormone stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a parathyroid hormone stimulus.
	GO:0071356	cellular response to tumor necrosis factor	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0070932	histone H3 deacetylation	The modification of histone H3 by the removal of one or more acetyl groups.
	GO:0070933	histone H4 deacetylation	The modification of histone H4 by the removal of one or more acetyl groups.
	GO:0016575	histone deacetylation	The modification of histones by removal of acetyl groups.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0045820	negative regulation of glycolytic process	Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis.
	GO:0010832	negative regulation of myotube differentiation	Any process that decreases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
	GO:0045668	negative regulation of osteoblast differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.
	GO:0043433	negative regulation of sequence-specific DNA binding transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0002076	osteoblast development	The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone.
	GO:0034983	peptidyl-lysine deacetylation	The removal of an acetyl group from an acetylated lysine residue in a peptide or protein.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0010592	positive regulation of lamellipodium assembly	Any process that increases the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
	GO:0043525	positive regulation of neuron apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
	GO:0033235	positive regulation of protein sumoylation	Any process that activates or increases the frequency, rate or extent of the addition of SUMO groups to a protein.
	GO:1903428	positive regulation of reactive oxygen species biosynthetic process	Any process that activates or increases the frequency, rate or extent of reactive oxygen species biosynthetic process.
	GO:0051091	positive regulation of sequence-specific DNA binding transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0014911	positive regulation of smooth muscle cell migration	Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.
	GO:0048661	positive regulation of smooth muscle cell proliferation	Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0010882	regulation of cardiac muscle contraction by calcium ion signaling	Any process that modulates the frequency, rate or extent of cardiac muscle contraction by changing the calcium ion signals that trigger contraction.
	GO:0040029	regulation of gene expression, epigenetic	Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.
	GO:0043393	regulation of protein binding	Any process that modulates the frequency, rate or extent of protein binding.
	GO:0048742	regulation of skeletal muscle fiber development	Any process that modulates the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
	GO:0051153	regulation of striated muscle cell differentiation	Any process that modulates the frequency, rate or extent of striated muscle cell differentiation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0014894	response to denervation involved in regulation of muscle adaptation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a denervation stimulus. This process occurs as part of the regulation of muscle adaptation.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0070555	response to interleukin-1	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
	GO:0001501	skeletal system development	The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0031672	A band	The dark-staining region of a sarcomere, in which myosin thick filaments are present; the center is traversed by the paler H zone, which in turn contains the M line.
	GO:0030018	Z disc	Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
	GO:0042641	actomyosin	Any complex of actin, myosin, and accessory proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0000118	histone deacetylase complex	A protein complex that possesses histone deacetylase activity.
	GO:0031594	neuromuscular junction	The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0030017	sarcomere	The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
	GO:0017053	transcriptional repressor complex	A protein complex that possesses activity that prevents or downregulates transcription.

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	2vqv
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	HDAC4_HUMAN \| P56524	:	2h8n 2o94 2vqj 2vqm 2vqo 2vqq 2vqw 3uxg 3uzd 3v31 4cbt 4cby 5a2s

2vqj	STRUCTURE OF HDAC4 CATALYTIC DOMAIN BOUND TO A TRIFLUOROMETHYLKETONE INHBITOR
2vqm	STRUCTURE OF HDAC4 CATALYTIC DOMAIN BOUND TO A HYDROXAMIC ACID INHBITOR
2vqo	STRUCTURE OF HDAC4 CATALYTIC DOMAIN WITH A GAIN-OF-FUNCTION MUATION BOUND TO A TRIFLUOROMETHYLKETONE INHBITOR
2vqq	STRUCTURE OF HDAC4 CATALYTIC DOMAIN (A DOUBLE CYSTEINE-TO-ALANINE MUTANT) BOUND TO A TRIFLUOROMETHYLKETONE INHBITOR
2vqw	STRUCTURE OF INHIBITOR-FREE HDAC4 CATALYTIC DOMAIN (WITH GAIN-OF-FUNCTION MUTATION HIS332TYR)

Description

Compounds

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Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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Exons (12, 24)

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Pfam Domains (2, 4)

Gene Ontology (74, 74)

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