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Title :   COMPLEX STRUCTURE OF PCAF BROMODOMAIN WITH SMALL CHEMICAL LIGAND NP1

Authors :   L. Zeng, J. Li, M. Muller, S. Yan, S. Mujtaba, C. Pan, Z. Wang, M. M. Zhou

Date :   07 Dec 04 (Deposition) - 16 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A

Keywords :   Bromodomain, Histone-Acetyltransferase, Nmr-Structure, Chemical Ligand (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Zeng, J. Li, M. Muller, S. Yan, S. Mujtaba, C. Pan, Z. Wang, M. M. Zhou
Selective Small Molecules Blocking Hiv-1 Tat And Coactivator Pcaf Association
J. Am. Chem. Soc. V. 127 2376 2005
PubMed-ID: 15724976 | Reference-DOI: 10.1021/JA044885G
(for further references see the PDB file header)

Molecule 1 - HISTONE ACETYLATRANSFERASE PCAF
	Chains	:	A
	EC Number	:	2.3.1.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET14B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	BROMODOMAIN
	Gene	:	PCAF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	P300/CBP-ASSOCIATED FACTOR, P/CAF, HISTONE ACETYLASE PCAF


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	NP1	1	Ligand/Ion	N-(3-AMINOPROPYL)-4-METHYL-2-NITROBENZENAMINE

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:750 , VAL A:752 , GLU A:756 , ALA A:757 , PRO A:758 , TYR A:802 , TYR A:809	BINDING SITE FOR RESIDUE NP1 A 201

(no "SS Bond" information available for 1WUG)

(no "Cis Peptide Bond" information available for 1WUG)

(no "SAP(SNP)/Variant" information available for 1WUG)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	KAT2B_HUMAN	740-810	1	A:740-810
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	KAT2B_HUMAN	745-802	1	A:745-802

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000263754	1a	ENSE00001189392	chr3:20081515-20082272	758	KAT2B_HUMAN	1-101	101	0	-	-
1.2	ENST00000263754	2	ENSE00001076225	chr3:20113825-20113951	127	KAT2B_HUMAN	102-144	43	0	-	-
1.3	ENST00000263754	3	ENSE00001695585	chr3:20136755-20136900	146	KAT2B_HUMAN	144-192	49	0	-	-
1.4	ENST00000263754	4	ENSE00001076230	chr3:20141354-20141446	93	KAT2B_HUMAN	193-223	31	0	-	-
1.6	ENST00000263754	6	ENSE00001076222	chr3:20142779-20142960	182	KAT2B_HUMAN	224-284	61	0	-	-
1.7b	ENST00000263754	7b	ENSE00000755284	chr3:20153088-20153279	192	KAT2B_HUMAN	284-348	65	0	-	-
1.8a	ENST00000263754	8a	ENSE00000755443	chr3:20156374-20156480	107	KAT2B_HUMAN	348-384	37	0	-	-
1.9	ENST00000263754	9	ENSE00000755498	chr3:20161090-20161215	126	KAT2B_HUMAN	384-426	43	0	-	-
1.10b	ENST00000263754	10b	ENSE00000755616	chr3:20164160-20164296	137	KAT2B_HUMAN	426-471	46	0	-	-
1.11	ENST00000263754	11	ENSE00000755725	chr3:20167397-20167605	209	KAT2B_HUMAN	472-541	70	0	-	-
1.12a	ENST00000263754	12a	ENSE00001800162	chr3:20168915-20169041	127	KAT2B_HUMAN	541-583	43	0	-	-
1.13	ENST00000263754	13	ENSE00001076216	chr3:20178434-20178544	111	KAT2B_HUMAN	584-620	37	0	-	-
1.14	ENST00000263754	14	ENSE00001076226	chr3:20181713-20181856	144	KAT2B_HUMAN	621-668	48	0	-	-
1.15a	ENST00000263754	15a	ENSE00001076221	chr3:20187808-20187922	115	KAT2B_HUMAN	669-707	39	0	-	-
1.16	ENST00000263754	16	ENSE00001076235	chr3:20189455-20189491	37	KAT2B_HUMAN	707-719	13	1	A:715-719	5
1.17b	ENST00000263754	17b	ENSE00001076223	chr3:20189735-20189798	64	KAT2B_HUMAN	719-740	22	1	A:719-740	22
1.18a	ENST00000263754	18a	ENSE00001076233	chr3:20189895-20189979	85	KAT2B_HUMAN	741-769	29	1	A:741-769	29
1.19	ENST00000263754	19	ENSE00001272618	chr3:20193824-20195896	2073	KAT2B_HUMAN	769-832	64	1	A:769-832	64

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:118
 aligned with KAT2B_HUMAN | Q92831 from UniProtKB/Swiss-Prot  Length:832

    Alignment length:118
                                   724       734       744       754       764       774       784       794       804       814       824        
          KAT2B_HUMAN   715 GKEKSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLIDK 832
               SCOP domains d1wuga_ A: P300/CAF histone acetyltransferase bromodomain                                                              SCOP domains
               CATH domains 1wugA00 A:715-832 Histone Acetyltransferase; Chain A                                                                   CATH domains
               Pfam domains -----------------Bromodomain-1wugA01 A:732-815                                                       ----------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhh..hhhhhh..................hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------BROMODOMAIN_2  PDB: A:740-810 UniProt: 740-810                         ---------------------- PROSITE (1)
                PROSITE (2) ------------------------------BROMODOMAIN_1  PDB: A:745-802 UniProt: 745-802            ------------------------------ PROSITE (2)
           Transcript 1 (1) 1.16 ---------------------Exon 1.18a  PDB: A:741-769   --------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.17b            ----------------------------Exon 1.19  PDB: A:769-832 UniProt: 769-832                       Transcript 1 (2)
                 1wug A 715 GSHMSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLIDK 832
                                   724       734       744       754       764       774       784       794       804       814       824

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Bromodomain-like (339)

Superfamily: Bromodomain (203)

Family: Bromodomain (34)

Protein domain: P300/CAF histone acetyltransferase bromodomain (8)

Human (Homo sapiens) [TaxId: 9606] (8)

d1wuga_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Histone Acetyltransferase; Chain A (22)

Homologous Superfamily: Histone Acetyltransferase; Chain A (22)

Human (Homo sapiens) (14)

1wugA00

A:715-832

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Bromodomain] (56)

Family: Bromodomain (56)

Homo sapiens (Human) (44)

Bromodomain-1wugA01

A:732-815

NMR Structure(hide GO term definitions)

Chain A (KAT2B_HUMAN | Q92831)

molecular function
	GO:0008080	N-acetyltransferase activity	Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	GO:0016407	acetyltransferase activity	Catalysis of the transfer of an acetyl group to an acceptor molecule.
	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:0004861	cyclin-dependent protein serine/threonine kinase inhibitor activity	Stops, prevents or reduces the activity of a cyclin-dependent protein serine/threonine kinase.
	GO:0004402	histone acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
	GO:0035035	histone acetyltransferase binding	Interacting selectively and non-covalently with the enzyme histone acetyltransferase.
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	GO:0004468	lysine N-acetyltransferase activity, acting on acetyl phosphate as donor	Catalysis of the reaction: acetyl phosphate + L-lysine = phosphate + N6-acetyl-L-lysine.
	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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	GO:0003712	transcription cofactor activity	Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory 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:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0018076	N-terminal peptidyl-lysine acetylation	The acetylation of the N-terminal lysine of proteins.
	GO:0007219	Notch signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0007050	cell cycle arrest	A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
	GO:0032869	cellular response to insulin 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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	GO:0034599	cellular response to oxidative stress	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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	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: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:0043966	histone H3 acetylation	The modification of histone H3 by the addition of an acetyl group.
	GO:0043970	histone H3-K9 acetylation	The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 9 of the histone.
	GO:0016573	histone acetylation	The modification of a histone by the addition of an acetyl group.
	GO:0018393	internal peptidyl-lysine acetylation	The addition of an acetyl group to a non-terminal lysine residue in a protein.
	GO:0007613	memory	The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0045736	negative regulation of cyclin-dependent protein serine/threonine kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
	GO:0018394	peptidyl-lysine acetylation	The acetylation of peptidyl-lysine.
	GO:0035563	positive regulation of chromatin binding	Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:0035948	positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of gluconeogenesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0071442	positive regulation of histone H3-K14 acetylation	Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone.
	GO:2000617	positive regulation of histone H3-K9 acetylation	Any process that activates or increases the frequency, rate or extent of histone H3-K9 acetylation.
	GO:0010976	positive regulation of neuron projection development	Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	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:0006473	protein acetylation	The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
	GO:0010835	regulation of protein ADP-ribosylation	Any process that modulates the frequency, rate or extent of protein ADP-ribosylation. Protein ADP-ribosylation is the transfer, from NAD, of ADP-ribose to protein amino acids.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0005671	Ada2/Gcn5/Ada3 transcription activator complex	A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues.
	GO:0031674	I band	A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
	GO:0000125	PCAF complex	A large multiprotein complex that possesses histone acetyltransferase activity and is involved in regulation of transcription. The composition is similar to that of the SAGA complex, but includes fewer Spt and Ada proteins, and more TAFs.
	GO:0042641	actomyosin	Any complex of actin, myosin, and accessory proteins.
	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:0000123	histone acetyltransferase complex	A protein complex that possesses histone acetyltransferase activity.
	GO:0000776	kinetochore	A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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.

NMR Structure
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1b91	STRUCTURE AND LIGAND OF A HISTONE ACETYLTRANSFERASE BROMODOMAIN
1jm4	RECOGNITION OF HIV-1 TAT BY PCAF BROMODOMAIN
1wum	THE SAME PROTEIN WITH SMALL CHEMICAL LIGAND NP2

Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

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Exons (4, 4)

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