2OD2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF YHST2 I117F MUTANT BOUND TO CARBA-NAD+ AND AN ACETYLATED H4 PEPTIDE

Authors :   B. D. Sanders

Date :   21 Dec 06 (Deposition) - 20 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Zn Binding Protein, Rossmann Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. D. Sanders, K. Zhao, J. T. Slama, R. Marmorstein
Structural Basis For Nicotinamide Inhibition And Base Exchange In Sir2 Enzymes.
Mol. Cell V. 25 463 2007
PubMed-ID: 17289592 | Reference-DOI: 10.1016/J.MOLCEL.2006.12.022

Molecule 1 - NAD-DEPENDENT DEACETYLASE HST2
	Chains	:	A
	EC Number	:	3.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET-A
	Expression System Strain	:	DE3 BL-21 GOLD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	HST2 CATALYTIC CORE DOMAIN, RESIDUES 1-294
	Gene	:	HST2
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	HOMOLOGOUS TO SIR2 PROTEIN 2

Molecule 2 - ACETYLATED H4 PEPTIDE
	Chains	:	B
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS (HUMANS)
	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 (4, 7)

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

Asymmetric Unit (6, 6)

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	GLY A:32 , ALA A:33 , GLY A:34 , THR A:37 , ARG A:45 , GLN A:115 , ASN A:116 , PHE A:117 , ASP A:118 , 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:2011 , HOH A:2015 , HOH A:2030 , HOH A:2076 , HOH A:2092 , HOH A:2095 , HOH A:2119 , ALY B:16	BINDING SITE FOR RESIDUE CNA A 1001
3	AC3	SOFTWARE	SER A:193 , TRP A:196 , GLU A:237 , LYS B:12	BINDING SITE FOR RESIDUE GOL A 1989
4	AC4	SOFTWARE	THR A:49 , GLY A:50 , HOH A:2004 , HOH A:2090	BINDING SITE FOR RESIDUE GOL A 1990
5	AC5	SOFTWARE	LYS A:84 , TYR A:87 , ASN A:90 , LEU A:159 , ALA A:160	BINDING SITE FOR RESIDUE GOL A 1991
6	AC6	SOFTWARE	LYS A:26 , LYS A:110 , TRP A:202 , LYS A:206	BINDING SITE FOR RESIDUE GOL A 1992

(no "SS Bond" information available for 2OD2)

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 2OD2)

Asymmetric Unit (1, 1)

	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

Biological Unit 1 (1, 1)

	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

Biological Unit 2 (1, 2)

	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

Asymmetric Unit (1, 1)

	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	1	A:1-293 (gaps)	293

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
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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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2od2A01 A:-2-37,A:94-134,A:190-293      2od2A02 A:38-93,A:135-189 SIR2/SIRT2 'Small Domain'     2od2A01 A:-2-37,A:94-134,A:190-293       2od2A02 A:38-93,A:135-189 SIR2/SIRT2 'Small Domain'    2od2A01 A:-2-37,A:94     -134,A:190-293 TPP-binding domain                                               CATH domains
               Pfam domains ----------------------------------SIR2-2od2A01 A:32-230                                                                                                                                                                                  --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh....eeeee.hhhhhhhh........hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....eehhhhhhhhhh................eeeee.......hhhhhhhhhhhhhhhhhhh..-----...eeeee.......hhhhhhhhh....eeeee.....hhhhhh.....eee..hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------SIRTUIN  PDB: A:13-286 UniProt: 13-286                                                                                                                                                                                                                                            ------- PROSITE
               Transcript 1 ---Exon 1.1  PDB: A:1-293 (gaps) UniProt: 1-357 [INCOMPLETE]                                                                                                                                                                                                                                             Transcript 1
                 2od2 A  -2 MASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNFDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITT-----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:7
                                       
               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 ------- Transcript
                 2od2 B  12 KGGAkRH  18
                                |  
                               16-ALY

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 2OD2)

Asymmetric 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)

2od2A02

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)

2od2A01

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)

SIR2-2od2A01

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.

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		Tyr A:229 - Pro A:230	[ RasMol ]

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	2od2
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	HST2_YEAST \| P53686	:	1q14 1q17 1q1a 1szc 1szd 2od7 2od9 2qqf 2qqg

1szc	WILDTYPE YHST2 BOUND TO CARBA-NAD+ AND AN ACETYLATED H4 PEPTIDE
1szd	WILDTYPE YHST2 BOUND TO ADP-RIBOSE AND AN ACETYLATED H4 PEPTIDE
2od7	CRYSTAL STRUCTURE OF YHST2 BOUND TO THE INTERMEDIATE ANALOGUE ADP-HPD, AND AND ACEYLATED H4 PEPTIDE
2od9	STRUCTURAL BASIS FOR NICOTINAMIDE INHIBITION AND BASE EXCHANGE IN SIR2 ENZYMES

Description

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Ligands, Modified Residues, Ions (4, 7)

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