1SZC - JenaLib

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Title :   STRUCTURAL BASIS FOR NICOTINAMIDE CLEAVAGE AND ADP-RIBOSE TRANSFER BY NAD+-DEPENDENT SIR2 HISTONE/PROTEIN DEACETYLASES

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

Date :   05 Apr 04 (Deposition) - 15 Jun 04 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Sir2, Sirtuin, Histone Deacetylase, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Zhao, R. Harshaw, X. Chai, R. Marmorstein
Structural Basis For Nicotinamide Cleavage And Adp-Ribose Transfer By Nad(+)-Dependent Sir2 Histone/Protein Deacetylases.
Proc. Natl. Acad. Sci. Usa V. 101 8563 2004
PubMed-ID: 15150415 | Reference-DOI: 10.1073/PNAS.0401057101
(for further references see the PDB file header)

Molecule 1 - NAD-DEPENDENT DEACETYLASE HST2
	Chains	:	A
	EC Number	:	3.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	HST2(1-294)
	Expression System Strain	:	BL21 (GOLD)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC CORE DOMAIN
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	HOMOLOGOUS TO SIR2 PROTEIN 2

Molecule 2 - HISTONE H4 PEPTIDE
	Chains	:	B
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE NATURALLY OCCURS IN SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 8)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	CNA	1	Ligand/Ion	CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	GOL	4	Ligand/Ion	GLYCEROL
5	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	CNA	1	Ligand/Ion	CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	GOL	4	Ligand/Ion	GLYCEROL
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	ALY	2	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	CNA	2	Ligand/Ion	CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	GOL	8	Ligand/Ion	GLYCEROL
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:143 , CYS A:146 , CYS A:170 , CYS A:173	BINDING SITE FOR RESIDUE ZN A 701
2	AC2	SOFTWARE	ARG A:204 , HOH A:2136	BINDING SITE FOR RESIDUE CL A 702
3	AC3	SOFTWARE	GLY A:32 , ALA A:33 , GLY A:34 , THR A:37 , ARG A:45 , GLN A:115 , ASN A:116 , ILE A:117 , ASP A:118 , PHE A:184 , GLY A:223 , THR A:224 , SER A:225 , ASN A:248 , LEU A:249 , GLN A:268 , TYR A:269 , SER A:270 , HOH A:2003 , HOH A:2005 , HOH A:2021 , HOH A:2029 , HOH A:2098 , HOH A:2100 , HOH A:2112 , HOH A:2133 , HOH A:2135 , HOH A:2202 , ALY B:16	BINDING SITE FOR RESIDUE CNA A 1001
4	AC4	SOFTWARE	SER A:193 , TRP A:196 , GLU A:237 , LYS B:12	BINDING SITE FOR RESIDUE GOL A 1989
5	AC5	SOFTWARE	THR A:49 , GLY A:50 , HOH A:2012 , HOH A:2115	BINDING SITE FOR RESIDUE GOL A 1990
6	AC6	SOFTWARE	LYS A:84 , ASN A:90 , LEU A:159 , ALA A:160 , HOH A:2260	BINDING SITE FOR RESIDUE GOL A 1991
7	AC7	SOFTWARE	LYS A:26 , LYS A:110 , TRP A:202 , LYS A:206 , HOH A:2164	BINDING SITE FOR RESIDUE GOL A 1992

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

Asymmetric Unit

No.	Residues
1	His A:162	-	Pro A:163
2	Tyr A:229	-	Pro A:230

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	HST2_YEAST	13-286	1	A:13-286
2	HISTONE_H4	PS00047	Histone H4 signature.	H4_YEAST	15-19	1	B:14-18

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	HST2_YEAST	13-286	1	A:13-286
2	HISTONE_H4	PS00047	Histone H4 signature.	H4_YEAST	15-19	1	B:14-18

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	HST2_YEAST	13-286	2	A:13-286
2	HISTONE_H4	PS00047	Histone H4 signature.	H4_YEAST	15-19	2	B:14-18

Asymmetric Unit (2, 2)

	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	1	B:12-19	8

2.1	YPL015C	1	YPL015C.1	XVI:526880-525807	1074	HST2_YEAST	1-357	357	1	A:1-293 (gaps)	293

Asymmetric Unit

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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:291
 aligned with HST2_YEAST | P53686 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:296
                               1                                                                                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287      
           HST2_YEAST     - ---MSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITTSGKHPQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTA 293
               SCOP domains d1szca_ A: Hst2                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1szcA01 A:-2-37,A:94-134,A:190-293      1szcA02 A:38-93,A:135-189 SIR2/SIRT2 'Small Domain'     1szcA01 A:-2-37,A:94-134,A:190-293       1szcA02 A:38-93,A:135-189 SIR2/SIRT2 'Small Domain'    1szcA01 A:-2-37,A:94     -134,A:190-293 TPP-binding domain                                               CATH domains
               Pfam domains ----------------------------------SIR2-1szcA01 A:32-230                                                                                                                                                                                  --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh....eeeee.hhhhhhhh........hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....ee.hhhhhhhh.................eeeee.......hhhhhhhhhhhhhhhhhhhh.-----...eeeee.......hhhhhhhhh.....eeee.....hhhhhh.....eee..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------SIRTUIN  PDB: A:13-286 UniProt: 13-286                                                                                                                                                                                                                                            ------- PROSITE
               Transcript 2 ---Exon 2.1  PDB: A:1-293 (gaps) UniProt: 1-357 [INCOMPLETE]                                                                                                                                                                                                                                             Transcript 2
                 1szc A  -2 MASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITT-----QQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTA 293
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207 |     217       227       237       247       257       267       277       287      
                                                                                                                                                                                                                                             209   215

Chain B from PDB  Type:PROTEIN  Length:8
 aligned with H4_YEAST | P02309 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:8
             H4_YEAST    13 KGGAKRHR  20
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                PROSITE (2) --HISTO- PROSITE (2)
               Transcript 1 Exon 1.1 Transcript 1
                 1szc B  12 KGGAkRHR  19
                                |   
                                |   
                               16-ALY

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	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(

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Superfamilies( (-)

)

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)

d1szca_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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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)

1szcA02

A:38-93,A:135-189

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

Topology: Rossmann fold (7312)

Homologous Superfamily: TPP-binding domain (120)

Baker's yeast (Saccharomyces cerevisiae) (20)

1szcA01

A:-2-37,A:94-134,A:190-293

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FAD_DHS (82)

Family: SIR2 (16)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (7)

SIR2-1szcA01

A:32-230

Asymmetric Unit(hide GO term definitions)

Chain A (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.

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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1q14	STRUCTURE AND AUTOREGULATION OF THE YEAST HST2 HOMOLOG OF SIR2
1q17	STRUCTURE OF THE YEAST HST2 PROTEIN DEACETYLASE IN TERNARY COMPLEX WITH 2'-O-ACETYL ADP RIBOSE AND HISTONE PEPTIDE

Description

Compounds

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Ligands, Modified Residues, Ions (5, 8)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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