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Title :   CRYSTAL STRUCTURE OF HUMAN SIRT3 WITH ACETYL-LYSINE ACECS2 PEPTIDE

Authors :   L. Jin, W. Wei, Y. Jiang, H. Peng, J. Cai, C. Mao, H. Dai, J. E. Bemis, M. R. J J. C. Milne, C. H. Westphal, R. B. Perni

Date :   12 Mar 09 (Deposition) - 16 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Nad Dependent Deacetylase, Sirtuin, Substrate Peptide Complex, Hydrolase, Metal-Binding, Mitochondrion, Nad, Transit Peptide, Ligase, Hydrolase-Hydrolase Regulator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Jin, W. Wei, Y. Jiang, H. Peng, J. Cai, C. Mao, H. Dai, W. Choy, J. E. Bemis, M. R. Jirousek, J. C. Milne, C. H. Westphal, R. B. Perni
Crystal Structures Of Human Sirt3 Displaying Substrate-Induced Conformational Changes.
J. Biol. Chem. V. 284 24394 2009
PubMed-ID: 19535340 | Reference-DOI: 10.1074/JBC.M109.014928

Molecule 1 - NAD-DEPENDENT DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
	Chains	:	A
	EC Number	:	3.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET21B
	Expression System Strain	:	BL21-GOLD(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	HUMAN SIRT3, RESIDUES 118-399
	Gene	:	SIRT3, SIR2L3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SIR2-LIKE PROTEIN 3, HSIRT3

Molecule 2 - ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL
	Chains	:	B
	EC Number	:	6.2.1.1
	Engineered	:	YES
	Fragment	:	ACECS2 PEPTIDE, RESIDUES 638-649
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ACETATE--COA LIGASE 2, ACETYL-COA SYNTHETASE 2, ACYL-COA SYNTHETASE SHORT-CHAIN FAMILY MEMBER 1
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 6)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	BCT	1	Ligand/Ion	BICARBONATE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	2	Ligand/Ion	SULFATE ION
5	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 10)

No.	Name	Count	Type	Full Name
1	ALY	2	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	BCT	2	Ligand/Ion	BICARBONATE ION
3	GOL	2	Ligand/Ion	GLYCEROL
4	SO4	4	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:256 , CYS A:259 , CYS A:280 , CYS A:283	BINDING SITE FOR RESIDUE ZN A 1
2	AC2	SOFTWARE	HOH A:18 , VAL A:277 , ARG A:279 , ARG A:384 , HOH A:466 , HOH A:501 , HOH A:522	BINDING SITE FOR RESIDUE SO4 A 3
3	AC3	SOFTWARE	ARG A:135 , GLN A:138 , LYS A:219 , GLU A:382	BINDING SITE FOR RESIDUE BCT A 4
4	AC4	SOFTWARE	HOH A:44 , HIS A:217 , GLY A:220 , LYS A:243 , HOH A:472	BINDING SITE FOR RESIDUE GOL A 5
5	AC5	SOFTWARE	HOH A:42 , PRO A:299 , GLN A:300 , SER B:640	BINDING SITE FOR RESIDUE SO4 B 2

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

Asymmetric Unit

No.	Residues
1	Gly A:121	-	Lys A:122
2	Glu A:325	-	Pro A:326

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051978	V	208	I	SIR3_HUMAN	Polymorphism	11246020	A	V	208	I
2	UniProt	VAR_051979	G	369	S	SIR3_HUMAN	Polymorphism	3020901	A	G	369	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051978	V	208	I	SIR3_HUMAN	Polymorphism	11246020	A	V	208	I
2	UniProt	VAR_051979	G	369	S	SIR3_HUMAN	Polymorphism	3020901	A	G	369	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	SIR3_HUMAN	126-382	1	A:126-382

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	SIR3_HUMAN	126-382	2	A:126-382

(no "Exon" information available for 3GLR)

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:274
 aligned with SIR3_HUMAN | Q9NTG7 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:274
                                   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    
           SIR3_HUMAN   121 GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKL 394
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....eeeee.hhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....eee...hhhhhhh............eeeee.......hhhhhhhhhhhhhh.eeeee.....ee.hhhhhhh......eeeee....hhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------- SAPs(SNPs)
                    PROSITE -----SIRTUIN  PDB: A:126-382 UniProt: 126-382                                                                                                                                                                                                                         ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3glr A 121 GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKL 394
                                   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

Chain B from PDB  Type:PROTEIN  Length:7
 aligned with ACS2L_HUMAN | Q9NUB1 from UniProtKB/Swiss-Prot  Length:689

    Alignment length:7
          ACS2L_HUMAN   639 RSGKVMR 645
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....ee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3glr B 639 RSGkVMR 645
                               |   
                               |   
                             642-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 3GLR)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (SIR3_HUMAN | Q9NTG7)

molecular function
	GO:0003950	NAD+ ADP-ribosyltransferase activity	Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
	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:0032041	NAD-dependent histone deacetylase activity (H3-K14 specific)	Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0009060	aerobic respiration	The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
	GO:0070932	histone H3 deacetylation	The modification of histone H3 by the removal of one or more acetyl groups.
	GO:0007005	mitochondrion organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
	GO:2000757	negative regulation of peptidyl-lysine acetylation	Any process that stops, prevents or reduces the frequency, rate or extent of peptidyl-lysine acetylation.
	GO:0034983	peptidyl-lysine deacetylation	The removal of an acetyl group from an acetylated lysine residue in a peptide or protein.
	GO:0006471	protein ADP-ribosylation	The transfer, from NAD, of ADP-ribose to protein amino acids.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Chain B (ACS2L_HUMAN | Q9NUB1)

molecular function
	GO:0016208	AMP binding	Interacting selectively and non-covalently with AMP, adenosine monophosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003987	acetate-CoA ligase activity	Catalysis of the reaction: ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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).
biological process
	GO:0019413	acetate biosynthetic process	The chemical reactions and pathways resulting in the formation of acetate, the anion of acetic acid.
	GO:0006085	acetyl-CoA biosynthetic process	The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated.
	GO:0019427	acetyl-CoA biosynthetic process from acetate	The chemical reactions and pathways resulting in the formation of acetyl-CoA from acetate, either directly or via acetylphosphate.
	GO:0006069	ethanol oxidation	An ethanol metabolic process in which ethanol is converted to acetyl-CoA via acetaldehyde and acetate.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0019542	propionate biosynthetic process	The chemical reactions and pathways resulting in the formation of propionate, the anion derived from propionic acid.
cellular component
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:325 - Pro A:326	[ RasMol ]
		Gly A:121 - Lys A:122	[ RasMol ]

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3gls	CRYSTAL STRUCTURE OF HUMAN SIRT3
3glt	CRYSTAL STRUCTURE OF HUMAN SIRT3 WITH ADPR BOUND TO THE ACECS2 PEPTIDE CONTAINING A THIOACETYL LYSINE
3glu	CRYSTAL STRUCTURE OF HUMAN SIRT3 WITH ACECS2 PEPTIDE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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