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Title :   CRYSTAL STRUCTURE OF YEAST ESA1 HAT DOMAIN COMPLEXED WITH H4K16COA BISUBSTRATE INHIBITOR

Authors :   H. Yuan, E. C. Ding, R. Marmorstein

Date :   04 Sep 11 (Deposition) - 09 Nov 11 (Release) - 18 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Acetyltransferase, Autoacetylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Yuan, D. Rossetto, H. Mellert, W. Dang, M. Srinivasan, J. Johnson, S. Hodawadekar, E. C. Ding, K. Speicher, N. Abshiru, R. Perry, J. Wu, C. Yang, Y. G. Zheng, D. W. Speicher, P. Thibault, A. Verreault, F. B. Johnson, S. L. Berger, R. Sternglanz, S. B. Mcmahon, J. Cote, R. Marmorstein
Myst Protein Acetyltransferase Activity Requires Active Sit Lysine Autoacetylation.
Embo J. V. 31 58 2011
PubMed-ID: 22020126 | Reference-DOI: 10.1038/EMBOJ.2011.382

Molecule 1 - HISTONE ACETYLTRANSFERASE ESA1
	Chains	:	A
	EC Number	:	2.3.1.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 160-435
	Gene	:	ESA1, YOR244W, O5257
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - HISTONE H4
	Chains	:	B
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 12-23
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	K16COA BISUBSTRATE INHIBITOR
	Synthetic	:	YES

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	CMC	1	Ligand/Ion	CARBOXYMETHYL COENZYME *A

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	ALY	3	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	CMC	3	Ligand/Ion	CARBOXYMETHYL COENZYME *A

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:3 , HOH A:4 , HOH A:48 , PHE A:258 , LEU A:259 , ALA A:303 , ILE A:305 , LEU A:306 , THR A:307 , GLN A:312 , ARG A:313 , MET A:314 , GLY A:315 , GLY A:317 , LYS A:318 , GLU A:338 , SER A:342 , SER A:348 , ARG A:421 , HOH B:52 , HOH B:246 , LYS B:500	BINDING SITE FOR RESIDUE CMC B 600

(no "SS Bond" information available for 3TO6)

Asymmetric Unit

No.	Residues
1	Lys A:339	-	Pro A:340

(no "SAP(SNP)/Variant" information available for 3TO6)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MYST_HAT	PS51726	MYST-type histone acetyltransferase (HAT) domain profile.	ESA1_YEAST	162-433	1	A:162-433

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MYST_HAT	PS51726	MYST-type histone acetyltransferase (HAT) domain profile.	ESA1_YEAST	162-433	3	A:162-433

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YNL030W	1	YNL030W.1	XIV:576729-577040	312	H4_YEAST	1-103	103	0	-	-

2.1	YOR244W	1	YOR244W.1	XV:792532-793869	1338	ESA1_YEAST	1-445	445	1	A:160-435	276

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:276
 aligned with ESA1_YEAST | Q08649 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:276
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429      
           ESA1_YEAST   160 EVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRKKCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCMTRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGSPEKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRYYKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPV 435
               SCOP domains d3to6a_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee..eee................eeee......ee.hhhhhhhhhh.........eeeee...eeeeeee...hhhhhhhhhhhhhh.............eeeeeeeeee..eeeeeeeeeee......eee..eee.hhhh..hhhhhhhhhhhhhhhhh....ee....hhhhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhh.hhhhhhhhhhhh..eeee..eeeee.hhhhhhhhhhhhhh.....hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --MYST_HAT  PDB: A:162-433 UniProt: 162-433                                                                                                                                                                                                                                       -- PROSITE
               Transcript 2 Exon 2.1  PDB: A:160-435 UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                                                                                 Transcript 2
                 3to6 A 160 EVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRKKCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLDHkTLYYDVDPFLFYCMTRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGSPEKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRYYKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPV 435
                                   169       179       189       199       209       219       229       239       249       259  |    269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429      
                                                                                                                                262-ALY

Chain B from PDB  Type:PROTEIN  Length:1
 aligned with H4_YEAST | P02309 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:1
             H4_YEAST   160 K  92
               SCOP domains - SCOP domains
               CATH domains - CATH domains
               Pfam domains - Pfam domains
         Sec.struct. author . Sec.struct. author
                 SAPs(SNPs) - SAPs(SNPs)
                    PROSITE - PROSITE
               Transcript 1 1 Transcript 1
                 3to6 B 160 K 500

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Acyl-CoA N-acyltransferases (Nat) (250)

Superfamily: Acyl-CoA N-acyltransferases (Nat) (250)

Family: N-acetyl transferase, NAT (154)

Protein domain: automated matches (23)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

d3to6a_

(no "CATH Domain" information available for 3TO6)

(no "Pfam Domain" information available for 3TO6)

Asymmetric Unit(hide GO term definitions)

Chain A (ESA1_YEAST | Q08649)

molecular function
	GO:0010485	H4 histone acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + histone H4 = CoA + acetyl-histone H4.
	GO:0004402	histone acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
	GO:0034212	peptide N-acetyltransferase activity	Catalysis of the acetylation of an amino acid residue of a peptide or protein, according to the reaction: acetyl-CoA + peptide = CoA + N-acetylpeptide.
	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: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:0016747	transferase activity, transferring acyl groups other than amino-acyl groups	Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006354	DNA-templated transcription, elongation	The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0043967	histone H4 acetylation	The modification of histone H4 by the addition of an acetyl group.
	GO:0016573	histone acetylation	The modification of a histone by the addition of an acetyl group.
	GO:0001207	histone displacement	The removal of histones, including histone dimers, from nucleosomes within chromatin.
	GO:0018394	peptidyl-lysine acetylation	The acetylation of peptidyl-lysine.
	GO:0016239	positive regulation of macroautophagy	Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.
	GO:0032968	positive regulation of transcription elongation from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
	GO:0051726	regulation of cell cycle	Any process that modulates the rate or extent of progression through the cell cycle.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0035267	NuA4 histone acetyltransferase complex	A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60).
	GO:0032777	Piccolo NuA4 histone acetyltransferase complex	A heterotrimeric H4/H2A histone acetyltransferase complex with a substrate preference of chromatin over free histones. It contains a subset of the proteins found in the larger NuA4 histone acetyltransferase complex; for example, the S. cerevisiae complex contains Esa1p, Yng2p, and Epl1p.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005724	nuclear telomeric heterochromatin	Heterochromatic regions of the chromosome found at the telomeres of a chromosome in the nucleus.

Chain B (H4_YEAST | P02309)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0034729	histone H3-K79 methylation	The modification of histone H3 by addition of a methyl group to lysine at position 79 of the histone.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0043935	sexual sporulation resulting in formation of a cellular spore	The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
	GO:0061587	transfer RNA gene-mediated silencing	The chromatin silencing that results in the inhibition of RNA polymerase II-transcribed genes located in the vicinity of tRNA genes.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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:0031298	replication fork protection complex	A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

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Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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Exons (1, 1)

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Gene Ontology (35, 36)

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