2H2G - JenaLib

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Title :   THE STRUCTURAL BASIS OF SIRTUIN SUBSTRATE AFFINITY

Authors :   M. S. Cosgrove, C. Wolberger

Date :   18 May 06 (Deposition) - 28 Nov 06 (Release) - 27 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

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

Keywords :   H3-K115Ac, Sir2, Sir2Tm, Sirtuin, Sirt1, Histone H3, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. S. Cosgrove, K. Bever, J. L. Avalos, S. Muhammad, X. Zhang, C. Wolberger
The Structural Basis Of Sirtuin Substrate Affinity
Biochemistry V. 45 7511 2006
PubMed-ID: 16768447 | Reference-DOI: 10.1021/BI0526332

Molecule 1 - NAD-DEPENDENT DEACETYLASE
	Chains	:	A
	EC Number	:	3.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	NPDA
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	REGULATORY PROTEIN SIR2 HOMOLOG

Molecule 2 - HISTONE H3 PEPTIDE
	Chains	:	B
	Engineered	:	YES
	Other Details	:	THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE (YEAST).
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ALY	-1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:124 , CYS A:127 , CYS A:148 , CYS A:151	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	HIS A:56 , GLU A:58 , HOH A:1134 , HIS B:113	BINDING SITE FOR RESIDUE ZN A 1002

(no "SS Bond" information available for 2H2G)

Asymmetric Unit

No.	Residues
1	Tyr A:194	-	Pro A:195

(no "SAP(SNP)/Variant" information available for 2H2G)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	NPD_THEMA	4-246	1	A:4-245

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	NPD_THEMA	4-246	1	A:4-245

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	NPD_THEMA	4-246	1	A:4-245

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YNL031C	1	YNL031C.1	XIV:576052-575642	411	H3_YEAST	1-136	136	1	B:113-117	5

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:236
 aligned with NPD_THEMA | Q9WYW0 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
            NPD_THEMA     1 MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDFRGPNGIYKKYSQNVFDIDFFYSHPEEFYRFAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKKVIELHGNVEEYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVFFGENLPQDALREAIGLSSRASLMIVLGSSLVVYPAAELPLITVRSGGKLVIVNLGETPFDDIATLKYNMDVVEFARRVMEEGGI 245
               SCOP domains d2h2ga_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains 2h2gA01 TPP-binding domain   2h2g         A02 A:30-75,A:117-165            2h2gA01 A:1-29,A:76-116,A:166-245        2h2gA02 A:30-75,A:117-165                        2h2gA01 A:1-29,A:76-116,A:166-245 TPP-binding domain                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..eeeee.hhhhhhhh....---------......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeee....hhhhhh....eee..eeeeeeee.....eeehhhhhhhh..............eeeee.......hhhhhhhhhhhhhhh.eeeee.....eehhhhhhhhhhhh..eeeee......hhhhh.eee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SIRTUIN  PDB: A:4-245 UniProt: 4-246                                                                                                                                                                                                               PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h2g A   1 MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDF---------YSQNVFDIDFFYSHPEEFYRFAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKKVIELHGNVEEYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVFFGENLPQDALREAIGLSSRASLMIVLGSSLVVYPAAELPLITVRSGGKLVIVNLGETPFDDIATLKYNMDVVEFARRVMEEGGI 245
                                    10        20        30  |      -  |     50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
                                                           33        43

Chain B from PDB  Type:PROTEIN  Length:5
 aligned with H3_YEAST | P61830 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:5
             H3_YEAST   114 HAKRV 118
               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 1 1.1   Transcript 1
                 2h2g B 113 HAkRV 117
                              |  
                              |  
                            115-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 '\|'

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: automated matches (36)

Protein domain: automated matches (36)

Thermotoga maritima [TaxId: 2336] (7)

d2h2ga_

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)

Thermotoga maritima. Organism_taxid: 2336. (13)

2h2gA02

A:30-75,A:117-165

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

Topology: Rossmann fold (7312)

Homologous Superfamily: TPP-binding domain (120)

Thermotoga maritima. Organism_taxid: 2336. (13)

2h2gA01

A:1-29,A:76-116,A:166-245

(no "Pfam Domain" information available for 2H2G)

Asymmetric Unit(hide GO term definitions)

Chain A (NPD_THEMA | Q9WYW0)

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:0034979	NAD-dependent protein deacetylase activity	Catalysis of the removal of one or more acetyl groups from a protein, requiring NAD.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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.

Chain B (H3_YEAST | P61830)

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:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0009303	rRNA transcription	The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
	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.
cellular component
	GO:0043505	CENP-A containing nucleosome	A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3).
	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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(no "Related Entries Specified in the PDB File" available for 2H2G)

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