3Q35 - JenaLib

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Title :   STRUCTURE OF THE RTT109-ACCOA/VPS75 COMPLEX AND IMPLICATIONS FOR CHAPERONE-MEDIATED HISTONE ACETYLATION

Authors :   Y. Tang, H. Yuan, K. Meeth, R. Marmorstein

Date :   21 Dec 10 (Deposition) - 02 Feb 11 (Release) - 23 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

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

Keywords :   Rtt109:Vps75=2:2 Stoichiometry Complex, Acetyl Coenzyme A (Acoa) Bound, Autoacetylation At Rtt109 Lys290, Nuclear, Transferase- Chaperone Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Tang, M. A. Holbert, N. Delgoshaie, H. Wurtele, B. Guillemette, K. Meeth, H. Yuan, P. Drogaris, E. H. Lee, C. Durette, P. Thibault, A. Verreault, P. A. Cole, R. Marmorstein
Structure Of The Rtt109-Accoa/Vps75 Complex And Implication For Chaperone-Mediated Histone Acetylation.
Structure V. 19 221 2011
PubMed-ID: 21256037 | Reference-DOI: 10.1016/J.STR.2010.12.012
(for further references see the PDB file header)

Molecule 1 - HISTONE ACETYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.3.1.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	6HIS-TEV-PCDF-DUET
	Expression System Strain	:	BL21(DE3) GOLD
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	KIM2, L1377, REM50, RTT109, YLL002W
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	REGULATOR OF TY1 TRANSPOSITION PROTEIN 109

Molecule 2 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	GST-TEV-PRSF-DUET
	Expression System Strain	:	BL21(DE3) GOLD
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-232
	Gene	:	N0890, VPS75, YNL246W
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ACO	1	Ligand/Ion	ACETYL COENZYME *A
2	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	ACO	2	Ligand/Ion	ACETYL COENZYME *A
2	ALY	2	Mod. Amino Acid	N(6)-ACETYLLYSINE
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:85 , SER A:86 , ALA A:88 , ASP A:89 , THR A:90 , VAL A:98 , VAL A:100 , ARG A:101 , PHE A:192 , ARG A:194 , PRO A:195 , ALA A:196 , TYR A:199 , LYS A:210 , HIS A:211 , LEU A:213 , TRP A:221 , TRP A:222 , EDO A:437	BINDING SITE FOR RESIDUE ACO A 999
2	AC2	SOFTWARE	SER A:86 , PHE A:192 , ARG A:194 , TYR A:199 , ACO A:999	BINDING SITE FOR RESIDUE EDO A 437

(no "SS Bond" information available for 3Q35)

(no "Cis Peptide Bond" information available for 3Q35)

(no "SAP(SNP)/Variant" information available for 3Q35)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RTT109_HAT	PS51728	Rtt109-type histone acetyltransferase (HAT) domain profile.	RT109_YEAST	2-404	1	A:2-404

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RTT109_HAT	PS51728	Rtt109-type histone acetyltransferase (HAT) domain profile.	RT109_YEAST	2-404	2	A:2-404

(no "Exon" information available for 3Q35)

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:394
 aligned with RT109_YEAST | Q07794 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:404
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400    
          RT109_YEAST     1 MSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGKVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYLQKVKPAIRSYKKISPELISAASTPARTLRILARRLKQSGSTVLKEIESPRFQQDLYLSFTCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQAKLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPKARFIHQLAEEDRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKSRKQFRAIKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREH 404
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --KAT11-3q35A01 A:3-404                                                                                                                                                                                                                                                                                                                                                                                              Pfam domains
         Sec.struct. author .hhhhhhhh......eeeeeeee...eee...............eeeeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeeeee........hhhhhhhhhhhhhhhh..hhhhh........----.........hhhhhhhhhhhhhhhh.......------..............eeeeeeee.........hhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh.......ee..........hhhhh......hhhhhhhhhhhhh......hhhhhhhhhhh..........eeeeeee...................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RTT109_HAT  PDB: A:2-404 UniProt: 2-404                                                                                                                                                                                                                                                                                                                                                                             PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q35 A   1 MSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGKVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYLQKVKPAIRS----SPELISAASTPARTLRILARRLKQSGSTVLKE------QQDLYLSFTCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQAKLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPkARFIHQLAEEDRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKSRKQFRAIKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREH 404
                                    10        20        30        40        50        60        70        80        90       100       110       120        |-   |   140       150       160    |    - |     180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400    
                                                                                                                                                          129  134                            165    172                                                                                                                   290-ALY

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with VPS75_YEAST | P53853 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:218
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
          VPS75_YEAST     9 NEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLEDE 226
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains NAP-3q35B01 B:9-220                                                                                                                                                                                                 ------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhh.eeeeeeee.hhh........eeeeeee.........eeeeeeeeee..-----..eeee........hhhhh.hhhhh....hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q35 B   9 NEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKKG-----DGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLEDE 226
                                    18        28        38        48        58        68        78        88        98       108       118       128 |     138       148       158       168       178       188       198       208       218        
                                                                                                                                                   130   136

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 3Q35)

(no "CATH Domain" information available for 3Q35)

Asymmetric Unit(hide GO term definitions)

Chain A (RT109_YEAST | Q07794)

molecular function
	GO:0010484	H3 histone acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + histone H3 = CoA + acetyl-histone H3.
	GO:0004402	histone acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
	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.
biological process
	GO:0006974	cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006303	double-strand break repair via nonhomologous end joining	The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	GO:0043966	histone H3 acetylation	The modification of histone H3 by the addition of an acetyl group.
	GO:0016573	histone acetylation	The modification of a histone by the addition of an acetyl group.
	GO:0043007	maintenance of rDNA	Any process involved in sustaining the fidelity and copy number of rDNA repeats.
	GO:0010526	negative regulation of transposition, RNA-mediated	Any process that decreases the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0043618	regulation of transcription from RNA polymerase II promoter in response to stress	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
	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: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.

Chain B (VPS75_YEAST | P53853)

molecular function
	GO:0010698	acetyltransferase activator activity	Binds to and increases the activity of an acetyltransferase, an enzyme which catalyzes the transfer of an acetyl group to an acceptor molecule.
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
biological process
	GO:0006303	double-strand break repair via nonhomologous end joining	The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	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:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	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:0035066	positive regulation of histone acetylation	Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0000785	chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
	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: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.

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	Cis Peptide Bonds
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Access by PDB/NDB ID
	3q35
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	RT109_YEAST \| Q07794
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	VPS75_YEAST \| P53853
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	2.3.1.48
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3d35	RTT109 D(130-179) BOUND WITH ACO
3dm7	VPS75 (1-232) HOMODIMER STRUCTURE
3q33	RTT109-VPS75 COMPLEX BOUND WITH ACO AND SOAKED WITH H3K9 PEPTIDE

Description

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Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

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