1Q17 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF THE YEAST HST2 PROTEIN DEACETYLASE IN TERNARY COMPLEX WITH 2'-O-ACETYL ADP RIBOSE AND HISTONE PEPTIDE

Authors :   K. Zhao, X. Chai, R. Marmorstein

Date :   18 Jul 03 (Deposition) - 18 Nov 03 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Histone Deacetylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Zhao, X. Chai, R. Marmorstein
Structure Of The Yeast Hst2 Protein Deacetylase In Ternary Complex With 2'-O-Acetyl Adp Ribose And Histone Peptide.
Structure V. 11 1403 2003
PubMed-ID: 14604530 | Reference-DOI: 10.1016/J.STR.2003.09.016
(for further references see the PDB file header)

Molecule 1 - HST2 PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	PROTEIN DEACETYLASE
	Gene	:	HST2 OR YPL015C OR LPA2C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	HOMOLOGOUS TO SIR2 PROTEIN 2

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	APR	3	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	CL	4	Ligand/Ion	CHLORIDE ION
3	ZN	3	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:143 , CYS A:146 , CYS A:170 , CYS A:173	BINDING SITE FOR RESIDUE ZN A 401
02	AC2	SOFTWARE	CYS B:143 , CYS B:146 , CYS B:170 , CYS B:173	BINDING SITE FOR RESIDUE ZN B 401
03	AC3	SOFTWARE	CYS C:143 , CYS C:146 , CYS C:170 , CYS C:173	BINDING SITE FOR RESIDUE ZN C 401
04	AC4	SOFTWARE	ARG C:204 , ARG C:240	BINDING SITE FOR RESIDUE CL C 701
05	AC5	SOFTWARE	TRP B:202	BINDING SITE FOR RESIDUE CL B 702
06	AC6	SOFTWARE	ARG A:204 , ARG A:240	BINDING SITE FOR RESIDUE CL A 703
07	AC7	SOFTWARE	ARG B:204 , ARG B:240	BINDING SITE FOR RESIDUE CL B 704
08	AC8	SOFTWARE	GLY A:32 , ALA A:33 , GLY A:34 , THR A:37 , ASP A:43 , PHE A:44 , ARG A:45 , TYR A:52 , GLN A:115 , HIS A:135 , GLY A:223 , THR A:224 , SER A:225 , VAL A:228 , ASN A:248 , LEU A:249 , GLU A:250 , GLN A:268 , TYR A:269 , SER A:270 , HOH A:1003 , HOH A:1025 , HOH A:1041	BINDING SITE FOR RESIDUE APR A 1001
09	AC9	SOFTWARE	GLY B:32 , ALA B:33 , GLY B:34 , THR B:37 , ASP B:43 , PHE B:44 , ARG B:45 , TYR B:52 , GLN B:115 , HIS B:135 , GLY B:223 , THR B:224 , SER B:225 , VAL B:228 , ASN B:248 , LEU B:249 , GLN B:268 , TYR B:269 , SER B:270 , HOH B:1007 , HOH B:1009 , HOH B:1023 , HOH B:1024 , HOH B:1046	BINDING SITE FOR RESIDUE APR B 1002
10	BC1	SOFTWARE	GLY C:32 , ALA C:33 , GLY C:34 , THR C:37 , ASP C:43 , PHE C:44 , ARG C:45 , TYR C:52 , GLN C:115 , HIS C:135 , GLY C:223 , THR C:224 , SER C:225 , VAL C:228 , ASN C:248 , LEU C:249 , GLN C:268 , TYR C:269 , SER C:270 , HOH C:1022	BINDING SITE FOR RESIDUE APR C 1003

(no "SS Bond" information available for 1Q17)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:229	-	Pro A:230
2	Tyr B:229	-	Pro B:230
3	Tyr C:229	-	Pro C:230

(no "SAP(SNP)/Variant" information available for 1Q17)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	HST2_YEAST	13-286	3	A:13-286 B:13-286 C:13-286

Asymmetric/Biological Unit (1, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YPL015C	1	YPL015C.1	XVI:526880-525807	1074	HST2_YEAST	1-357	357	3	A:1-294 (gaps) B:1-294 (gaps) C:1-294 (gaps)	294 294 294

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:290
 aligned with HST2_YEAST | P53686 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:298
                                1                                                                                                                                                                                                                                                                                                     
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286        
           HST2_YEAST     - ----MSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITTSGKHPQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTAQ 294
               SCOP domains d1q17a_ A: Hst2                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1q17A01 A:-3-37,A:94-134,A:190-294       1q17A02 A:38-93,A:135-189 SIR2/SIRT2 'Small Domain'     1q17A01 A:-3-37,A:94-134,A:190-294       1q17A02 A:38-93,A:135-189 SIR2/SIRT2 'Small Domain'    1q17A01 A:-3-37,A:        94-134,A:190-294 TPP-binding domain                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...hhhhhhhhhhhhhhhh....eeeee.hhhhh............hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....ee.hhhhhhhhhh...............eeeee.......hhhhhhhhhhhhhhhhhh.--------..eeeee.....eehhhhhhhhh....eeeee....hhhhh.......eee..hhhhhhhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------SIRTUIN  PDB: A:13-286 UniProt: 13-286                                                                                                                                                                                                                                            -------- PROSITE
               Transcript 1 ----Exon 1.1  PDB: A:1-294 (gaps) UniProt: 1-357 [INCOMPLETE]                                                                                                                                                                                                                                              Transcript 1
                 1q17 A  -3 GMASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKI--------QPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTAQ 294
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206|      216       226       236       246       256       266       276       286        
                                                                                                                                                                                                                                            207      216

Chain B from PDB  Type:PROTEIN  Length:294
 aligned with HST2_YEAST | P53686 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:300
                                  1                                                                                                                                                                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294
           HST2_YEAST     - ------MSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITTSGKHPQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTAQ 294
               SCOP domains d1q17b_ B: Hst2                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --1q17B01 B:-3-37,B:94-134,B:190-294       1q17B02 B:38-93,B:135-189 SIR2/SIRT2 'Small Domain'     1q17B01 B:-3-37,B:94-134,B:190-294       1q17B02 B:38-93,B:135-189 SIR2/SIRT2 'Small Domain'    1q17B01 B:-3-37,B:      94-134,B:190-294 TPP-binding domain                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee...hhhhhhhhhhhhhhhh....eeeee.hhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....ee.hhhhhhhhhh...............eeeee.......hhhhhhhhhhhhhhhhhhh------....eeeee.....eehhhhhhhhh.....eeee....hhhhhhh.....eee..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------SIRTUIN  PDB: B:13-286 UniProt: 13-286                                                                                                                                                                                                                                            -------- PROSITE
               Transcript 1 ------Exon 1.1  PDB: B:1-294 (gaps) UniProt: 1-357 [INCOMPLETE]                                                                                                                                                                                                                                              Transcript 1
                 1q17 B  -5 HHGMASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKI------PQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTAQ 294
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204  |    214       224       234       244       254       264       274       284       294
                                                                                                                                                                                                                                              207    214

Chain C from PDB  Type:PROTEIN  Length:295
 aligned with HST2_YEAST | P53686 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:299
                                 1                                                                                                                                                                                                                                                                                                     
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285         
           HST2_YEAST     - -----MSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITTSGKHPQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTAQ 294
               SCOP domains d1q17c_ C: Hst2                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1q17C01 C:-3-37,C:94-134,C:190-294       1q17C02 C:38-93,C:135-189 SIR2/SIRT2 'Small Domain'     1q17C01 C:-3-37,C:94-134,C:190-294       1q17C02 C:38-93,C:135-189 SIR2/SIRT2 'Small Domain'    1q17C01 C:-3-37,C:    94-134,C:190-294 TPP-binding domain                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee...hhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....ee.hhhhhhh..................eeeee.......hhhhhhhhhhhhhhhhh..----.......eeee.....eehhhhh.........eeee....hhhhhh......eee..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------SIRTUIN  PDB: C:13-286 UniProt: 13-286                                                                                                                                                                                                                                            -------- PROSITE
               Transcript 1 -----Exon 1.1  PDB: C:1-294 (gaps) UniProt: 1-357 [INCOMPLETE]                                                                                                                                                                                                                                              Transcript 1
                 1q17 C  -4 HGMASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKI----KHPQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTAQ 294
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205 |    |215       225       235       245       255       265       275       285         
                                                                                                                                                                                                                                             207  212

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/Biological Unit

Classes(

)

Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: DHS-like NAD/FAD-binding domain (176)

Superfamily: DHS-like NAD/FAD-binding domain (176)

Family: Sir2 family of transcriptional regulators (31)

Protein domain: Hst2 (5)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (5)

1a	d1q17a_	A:
1b	d1q17b_	B:
1c	d1q17c_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: SIR2/SIRT2 'Small Domain' (25)

Homologous Superfamily: SIR2/SIRT2 'Small Domain' (25)

Baker's yeast (Saccharomyces cerevisiae) (10)

1a	1q17A02	A:38-93,A:135-189
1b	1q17B02	B:38-93,B:135-189
1c	1q17C02	C:38-93,C:135-189

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: TPP-binding domain (120)

Baker's yeast (Saccharomyces cerevisiae) (20)

2a	1q17A01	A:-3-37,A:94-134,A:190-294
2b	1q17B01	B:-3-37,B:94-134,B:190-294
2c	1q17C01	C:-3-37,C:94-134,C:190-294

(no "Pfam Domain" information available for 1Q17)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (HST2_YEAST | P53686)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0070403	NAD+ binding	Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0017136	NAD-dependent histone deacetylase activity	Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone.
	GO:0046970	NAD-dependent histone deacetylase activity (H4-K16 specific)	Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein.
	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:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0001300	chronological cell aging	The process associated with progression of the cell from its inception to the end of its lifespan that occurs when the cell is in a non-dividing, or quiescent, state.
	GO:0070933	histone H4 deacetylation	The modification of histone H4 by the removal of one or more acetyl groups.
	GO:0031939	negative regulation of chromatin silencing at telomere	Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing at telomeres.
	GO:0045950	negative regulation of mitotic recombination	Any process that inhibits or decreases the rate of DNA recombination during mitosis.
	GO:0006476	protein deacetylation	The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular 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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Tyr A:229 - Pro A:230	[ RasMol ]
		Tyr B:229 - Pro B:230	[ RasMol ]
		Tyr C:229 - Pro C:230	[ RasMol ]

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Access by PDB/NDB ID
	1q17
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	HST2_YEAST \| P53686
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UniProtKB/Swiss-Prot
	HST2_YEAST \| P53686	:	1q14 1q1a 1szc 1szd 2od2 2od7 2od9 2qqf 2qqg

1q14	THE FULL LENGTH APO STRUCTURE

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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