1ICI - JenaLib

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Title :   CRYSTAL STRUCTURE OF A SIR2 HOMOLOG-NAD COMPLEX

Authors :   J. Min, J. Landry, R. Sternglanz, R. -M. Xu

Date :   01 Apr 01 (Deposition) - 02 May 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: B  (2x)

Keywords :   Rossmann Fold, Zinc Ribbon, Protein Deacetylase, Nad-Binding, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Min, J. Landry, R. Sternglanz, R. M. Xu
Crystal Structure Of A Sir2 Homolog-Nad Complex.
Cell(Cambridge, Mass. ) V. 105 269 2001
PubMed-ID: 11336676 | Reference-DOI: 10.1016/S0092-8674(01)00317-8

Molecule 1 - TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	XL1 BLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AF1676
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A
Biological Unit 3 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:124 , CYS A:127 , CYS A:145 , CYS A:148	BINDING SITE FOR RESIDUE ZN A 2001
2	AC2	SOFTWARE	CYS B:124 , CYS B:127 , CYS B:145 , CYS B:148	BINDING SITE FOR RESIDUE ZN B 2002
3	AC3	SOFTWARE	GLY A:20 , ALA A:21 , GLY A:22 , GLU A:26 , PHE A:32 , PRO A:44 , GLN A:98 , HIS A:116 , GLY A:185 , THR A:186 , SER A:187 , VAL A:190 , ASN A:211 , PRO A:212 , ASP A:213 , LYS A:228 , ALA A:229 , HOH A:2018 , HOH A:2029 , HOH A:2030 , HOH A:2032 , HOH A:2038 , HOH A:2054 , HOH A:2055 , HOH A:2057 , HOH A:2086 , HOH A:2097 , HOH A:2117	BINDING SITE FOR RESIDUE NAD A 1001
4	AC4	SOFTWARE	GLY B:20 , ALA B:21 , GLY B:22 , GLU B:26 , PHE B:32 , PRO B:44 , GLN B:98 , HIS B:116 , GLY B:185 , THR B:186 , SER B:187 , VAL B:190 , ASN B:211 , PRO B:212 , ASP B:213 , LYS B:228 , ALA B:229 , HOH B:2011 , HOH B:2016 , HOH B:2023 , HOH B:2033 , HOH B:2036 , HOH B:2059 , HOH B:2081 , HOH B:2107 , HOH B:2120	BINDING SITE FOR RESIDUE NAD B 1002

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

Asymmetric Unit

No.	Residues
1	Gln A:191	-	Pro A:192
2	Gln B:191	-	Pro B:192

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	NPD1_ARCFU	3-245	2	A:3-245 B:3-245

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	NPD1_ARCFU	3-245	2	A:3-245 B:3-245

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	NPD1_ARCFU	3-245	2	A:3-245 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIRTUIN	PS50305	Sirtuin catalytic domain profile.	NPD1_ARCFU	3-245	2	- B:3-245

(no "Exon" information available for 1ICI)

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:256
 aligned with NPD1_ARCFU | O28597 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:256
                                       1                                                                                                                                                                                                                                                    
                                     - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239      
           NPD1_ARCFU     - -----------MDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDDLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWFGEMLPPDVLDRAMREVERADVIIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALS 245
               SCOP domains d1icia_ A: AF1676, Sir2 homolog (Sir2-AF1?)                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhh...eeeee.hhhhhhhh..............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eee...................eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh..eeeee......hhhhh.eee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------SIRTUIN  PDB: A:3-245 UniProt: 3-245                                                                                                                                                                                                                PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ici A -10 GSHHHHHHGSHMDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDDLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWFGEMLPPDVLDRAMREVERADVIIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALS 245
                                    -1         9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with NPD1_ARCFU | O28597 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
           NPD1_ARCFU     2 DEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDDLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWFGEMLPPDVLDRAMREVERADVIIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALS 245
               SCOP domains d1icib_ B: AF1676, Sir2 homolog (Sir2-AF1?)                                                                                                                                                                                                          SCOP domains
               CATH domains 1iciB01 TPP-binding domain 1iciB02 B:29-75,B:117-162                      1iciB01 B:2-28,B:76-116,B:163-245        1iciB02 B:29-75,B:117-162                     1iciB01 B:2-28,B:76-116,B:163-245 TPP-binding domain                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...eeeee.hhhhhhhh..............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..eeeeee....hhhhhh....eee..eeeeeeee.....eee...................eeeee.......hhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhh..eeeee......hhhhh.eee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SIRTUIN  PDB: B:3-245 UniProt: 3-245                                                                                                                                                                                                                PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ici B   2 DEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDDLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWFGEMLPPDVLDRAMREVERADVIIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALS 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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(

)

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: AF1676, Sir2 homolog (Sir2-AF1?) (6)

Archaeoglobus fulgidus [TaxId: 2234] (6)

1a	d1icia_	A:
1b	d1icib_	B:

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)

Archaeoglobus fulgidus. Organism_taxid: 2234. (1)

1iciB02

B:29-75,B:117-162

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

Topology: Rossmann fold (7312)

Homologous Superfamily: TPP-binding domain (120)

Archaeoglobus fulgidus. Organism_taxid: 2234. (2)

1iciB01

B:2-28,B:76-116,B:163-245

(no "Pfam Domain" information available for 1ICI)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NPD1_ARCFU | O28597)

molecular function
	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:0036054	protein-malonyllysine demalonylase activity	Catalysis of the reaction: protein-malonyllysine + H2O => protein-lysine + malonate. This reaction is the removal of a malonyl group (CO-CH2-CO) from a malonylated lysine residue of a protein or peptide.
	GO:0036055	protein-succinyllysine desuccinylase activity	Catalysis of the reaction: protein-succinyllysine + H2O => protein-lysine + succinate. This reaction is the removal of a succinyl group (CO-CH2-CH2-CO) from a succinylated lysine residue of a protein or peptide.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0036047	peptidyl-lysine demalonylation	The process of removing a malonyl group (CO-CH2-CO) from an malonylated lysine residue in a peptide or protein.
	GO:0036049	peptidyl-lysine desuccinylation	The removal of a succinyl group (CO-CH2-CH2-CO) from a succinylated lysine residue in a peptide or protein.
	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:0036048	protein desuccinylation	The removal of a succinyl group (CO-CH2-CH2-CO) from a residue in a peptide or protein.
	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.

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	NPD1_ARCFU \| O28597	:	1m2g 1m2h 1m2j 1m2k 1m2n 4twi

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