3ZG6 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE NOVEL DE-LONG CHAIN FATTY ACID FUNCTION OF HUMAN SIRT6

Authors :   Y. Wang, Q. Hao

Date :   15 Dec 12 (Deposition) - 03 Apr 13 (Release) - 17 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,F

Keywords :   Hydrolase-Inhibitor Complex, Sirtuin Class Iii, Hdacs Nad Dependent (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Jiang, S. Khan, Y. Wang, G. Charron, B. He, C. Sebastian, J. Du, R. Kim E. Ge, R. Mostoslavsky, H. C. Hang, Q. Hao, H. Lin
Sirt6 Regulates Tnf-Alpha Secretion Through Hydrolysis Of Long-Chain Fatty Acyl Lysine
Nature V. 496 110 2013
PubMed-ID: 23552949 | Reference-DOI: 10.1038/NATURE12038

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-6
	Chains	:	A
	EC Number	:	3.5.1.-, 2.4.2.31
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 1-296
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	REGULATORY PROTEIN SIR2 HOMOLOG 6, SIR2-LIKE PROTEIN 6, SIRT6

Molecule 2 - PEPTIDE
	Chains	:	F
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630

		1	2
Asymmetric/Biological Unit	:	A	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	APR	1	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MYK	1	Mod. Amino Acid	N~6~-TETRADECANOYL-L-LYSINE
4	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:139 , CYS A:142 , CYS A:164 , CYS A:175	BINDING SITE FOR RESIDUE ZN A1295
2	AC2	SOFTWARE	GLY A:50 , ALA A:51 , GLY A:52 , THR A:55 , ASP A:61 , PHE A:62 , ARG A:63 , TRP A:69 , GLN A:111 , HIS A:131 , GLY A:212 , THR A:213 , SER A:214 , ILE A:217 , ASN A:238 , LEU A:239 , GLN A:240 , GLY A:254 , TYR A:255 , VAL A:256 , GOL A:1299 , HOH A:2019 , HOH A:2033 , HOH A:2041 , HOH A:2061 , HOH A:2145 , HOH A:2146	BINDING SITE FOR RESIDUE APR A1296
3	AC3	SOFTWARE	GLU A:187 , HIS A:244 , ARG A:246 , HIS A:247 , TRP F:15	BINDING SITE FOR RESIDUE GOL A1298
4	AC4	SOFTWARE	GLU A:20 , THR A:55 , ASP A:61 , PRO A:65 , APR A:1296 , HOH A:2018 , HOH A:2019 , HOH A:2040	BINDING SITE FOR RESIDUE GOL A1299

(no "SS Bond" information available for 3ZG6)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:3	-	Ala A:4
2	Arg A:218	-	Pro A:219

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_017154	S	46	N	SIR6_HUMAN	Polymorphism	352493	A	S	44	N

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	SIR6_HUMAN	35-274	1	A:33-272

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000359303	2b	ENSE00001974165	chr6:27858570-27858160	411	H31_HUMAN	1-136	136	1	F:4-15 (gaps)	38

Asymmetric/Biological 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:294
 aligned with SIR6_HUMAN | Q8N6T7 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:294
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292    
           SIR6_HUMAN     3 VNYAAGLSPYADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPK 296
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh........hhhhhhhh...............hhhhhhhhhhhhh....eeee....hhhhhh..hhh.eee......eeee.....eee...........eeeee..............eeee.........hhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhh.eeeee......hhhhh.eee..hhhhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------SIRTUIN  PDB: A:33-272 UniProt: 35-274                                                                                                                                                                                                          ---------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zg6 A   1 MNYAAGLSPYADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPK 294
                                    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

Chain F from PDB  Type:PROTEIN  Length:12
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:38
                                    14        24        34        
            H31_HUMAN     5 KQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRY  42
               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 1 Exon 1.2b  PDB: F:4-15 (gaps)          Transcript 1
                 3zg6 F   4 KQTARkSTGG--------------------------WW  15
                                 |  13         -         -      | 
                                 9-MYK                         14

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 3ZG6)

(no "CATH Domain" information available for 3ZG6)

(no "Pfam Domain" information available for 3ZG6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SIR6_HUMAN | Q8N6T7)

molecular function
	GO:0003956	NAD(P)+-protein-arginine ADP-ribosyltransferase activity	Catalysis of the reaction: NAD(P)+ + L-arginine = nicotinamide + N2-(ADP-D-ribosyl)-L-arginine.
	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: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:0046969	NAD-dependent histone deacetylase activity (H3-K9 specific)	Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein.
	GO:0034979	NAD-dependent protein deacetylase activity	Catalysis of the removal of one or more acetyl groups from a protein, requiring NAD.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	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:0033558	protein deacetylase activity	Catalysis of the hydrolysis of an acetyl group or groups from a protein substrate.
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006284	base-excision repair	In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
	GO:0042593	glucose homeostasis	Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
	GO:1990619	histone H3-K9 deacetylation	The modification of histone H3 by the removal of an acetyl group from lysine at position 9 of the histone.
	GO:0061647	histone H3-K9 modification	The modification of histone H3 at a lysine in position 9 of the histone.
	GO:0016575	histone deacetylation	The modification of histones by removal of acetyl groups.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0046325	negative regulation of glucose import	Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.
	GO:0045820	negative regulation of glycolytic process	Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	GO:2000648	positive regulation of stem cell proliferation	Any process that activates or increases the frequency, rate or extent of stem cell proliferation.
	GO:0003247	post-embryonic cardiac muscle cell growth involved in heart morphogenesis	The growth of a cardiac muscle cell during the postembryonic period that contributes to the shaping of the heart.
	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.
	GO:0031648	protein destabilization	Any process that decreases the stability of a protein, making it more vulnerable to degradative processes or aggregation.
	GO:0010569	regulation of double-strand break repair via homologous recombination	Any process that modulates the frequency, rate or extent of the error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences.
	GO:0031667	response to nutrient levels	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005724	nuclear telomeric heterochromatin	Heterochromatic regions of the chromosome found at the telomeres of a chromosome in the nucleus.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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 F (H31_HUMAN | P68431)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.
	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:0006335	DNA replication-dependent nucleosome assembly	The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0045814	negative regulation of gene expression, epigenetic	Any epigenetic process that stops, prevents or reduces the rate of gene expression.
	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:0002230	positive regulation of defense response to virus by host	Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
	GO:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:0051290	protein heterotetramerization	The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
	GO:0060968	regulation of gene silencing	Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
	GO:0032200	telomere organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
	GO:0098792	xenophagy	The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:218 - Pro A:219	[ RasMol ]
		Tyr A:3 - Ala A:4	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3ZG6)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (1, 1)

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