1S5P - JenaLib

Title :   STRUCTURE AND SUBSTRATE BINDING PROPERTIES OF COBB, A SIR2 HOMOLOG PROTEIN DEACETYLASE FROM ESCHERICIA COLI.

Authors :   K. Zhao, X. Chai, R. Marmorstein

Date :   21 Jan 04 (Deposition) - 23 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.96

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

Keywords :   Protein Deacetylase, Sir2 Homologue, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Zhao, X. Chai, R. Marmorstein
Structure And Substrate Binding Properties Of Cobb, A Sir2 Homolog Protein Deacetylase From Eschericia Coli.
J. Mol. Biol. V. 337 731 2004
PubMed-ID: 15019790 | Reference-DOI: 10.1016/J.JMB.2004.01.060
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:225
 aligned with NPD_ECOLI | P75960 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:235
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269     
            NPD_ECOLI    40 KPRVLVLTGAGISAESGIRTFRAADGLWEEHRVEDVATPEGFDRDPELVQAFYNARRRQLQQPEIQPNAAHLALAKLQDALGDRFLLVTQNIDNLHERAGNTNVIHMHGELLKVRCSQSGQVLDWTGDVTPEDKCHCCQFPAPLRPHVVWFGEMPLGMDEIYMALSMADIFIAIGTSGHVYPAAGFVHEAKLHGAHTVELNLEPSQVGNEFAEKYYGPASQVVPEFVEKLLKGLK 274
               SCOP domains d1s5pa_ A: NAD-dependent deacetylase CobB                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains SIR2-1s5pA01 A:40-184                                                                                                                            -------------------------------------------------------------   -------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhh.........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeee....hhhhhhh....ee..eeeeeeee.....eee...........-------.eeeee........hhhhhhhhhhhh.eeeee.....eehhhhhhhhhhhh..eeeeee.....---...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5p A  40 KPRVLVLTGAGISAESGIRTFRAADGLWEEHRVEDVATPEGFDRDPELVQAFYNARRRQLQQPEIQPNAAHLALAKLQDALGDRFLLVTQNIDNLHERAGNTNVIHMHGELLKVRCSQSGQVLDWTGDVTPEDKC-------PLRPHVVWFGEMPLGMDEIYMALSMADIFIAIGTSGHVYPAAGFVHEAKLHGAHTVELNLEPSQ---EFAEKYYGPASQVVPEFVEKLLKGLK 274
                                    49        59        69        79        89        99       109       119       129       139       149       159       169    |    -  |    189       199       209       219       229       239     | 249       259       269     
                                                                                                                                                                174     182                                                            245 249

Chain B from PDB  Type:PROTEIN  Length:8
                                        
               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
                 1s5p B  12 KGGAkRHR  19
                                |   
                               16-ALY

Legend:		→ Mismatch	(orange background)
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		→ 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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NPD_ECOLI | P75960)

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: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: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:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0034983	peptidyl-lysine deacetylation	The removal of an acetyl group from an acetylated lysine residue in a peptide or protein.
	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.
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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