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Title :   CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH SUCCINYLATED CPS1-PEPTIDE

Authors :   M. Pannek, M. Gertz, C. Steegborn

Date :   21 Jul 14 (Deposition) - 20 Aug 14 (Release) - 08 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Hydrolase, Regulatory Enzyme, Rossmann-Fold, Zinc-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Roessler, T. Nowak, M. Pannek, M. Gertz, G. T. Nguyen, M. Scharfe, I. Born, W. Sippl, C. Steegborn, M. Schutkowski
Chemical Probing Of The Human Sirtuin 5 Active Site Reveals Its Substrate Acyl Specificity And Peptide-Based Inhibitors.
Angew. Chem. Int. Ed. Engl. V. 53 10728 2014
PubMed-ID: 25111069 | Reference-DOI: 10.1002/ANIE.201402679

Molecule 1 - NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
	Chains	:	A, B
	EC Number	:	3.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	CODONPLUS
	Expression System Vector	:	PET151
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC CORE, RESIDUES 30-298
	Organism Common	:	ZEBRAFISH
	Organism Scientific	:	DANIO RERIO
	Organism Taxid	:	7955
	Synonym	:	REGULATORY PROTEIN SIR2 HOMOLOG 5, SIRTUIN 5

Molecule 2 - SUCCINYL-CPS1-PEPTIDE
	Chains	:	D
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 7)

No.	Name	Count	Type	Full Name
1	BEZ	1	Mod. Amino Acid	BENZOIC ACID
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
5	SLL	1	Mod. Amino Acid	(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC ACID
6	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	BEZ	1	Mod. Amino Acid	BENZOIC ACID
2	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
5	SLL	1	Mod. Amino Acid	(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC ACID
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	BEZ	-1	Mod. Amino Acid	BENZOIC ACID
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
5	SLL	-1	Mod. Amino Acid	(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC ACID
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:229 , GLU A:232 , THR B:65 , ALA B:78 , ALA B:82 , ARG B:101 , HIS B:154 , VAL B:217 , PHE B:219 , GLU B:221 , EDO B:1302	BINDING SITE FOR RESIDUE EPE B1299
2	AC2	SOFTWARE	CYS B:162 , CYS B:165 , CYS B:203 , CYS B:208	BINDING SITE FOR RESIDUE ZN B1300
3	AC3	SOFTWARE	CYS A:162 , CYS A:165 , CYS A:203 , CYS A:208	BINDING SITE FOR RESIDUE ZN A1300
4	AC4	SOFTWARE	ARG A:144 , ALA A:145 , ARG B:144 , ALA B:145	BINDING SITE FOR RESIDUE DMS B1301
5	AC5	SOFTWARE	GLN B:136 , ASN B:137 , ILE B:138 , EPE B:1299	BINDING SITE FOR RESIDUE EDO B1302

Asymmetric Unit

No.	Residues
1	A:274	-	B:274

Asymmetric Unit

No.	Residues
1	Ser A:174	-	Pro A:175
2	Tyr A:251	-	Pro A:252
3	Ser B:174	-	Pro B:175
4	Tyr B:251	-	Pro B:252

(no "SAP(SNP)/Variant" information available for 4UTN)

(no "PROSITE Motif" information available for 4UTN)

(no "Exon" information available for 4UTN)

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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.eeeeee.hhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee........eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utn A  35 DLTAFREHFAKAKHIAIITGAGVSAESGVPTFRGPGGFWRKWQAQDLATPEAFSRDPSLVWEFYHYRREVMRSKMPNPAHLAIAECEARLGQQGRSVVIITQNIDELHHRAGSKHVYEIHGSLFKTRCMSCGEVKANHKSPICPALDGKGAPDPNTKEARIPVELLPRCERKSCNGLLRPHVVWFGETLDSDILTAVERELEKCDLCLVVGTSSIVYPAAMFAPQVASRGVPVAEFNMECTPATKYHFEGPCGSTLPPALE 298
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   ||  287       297 
                                                                                                                                                                                                                                                                             278|                
                                                                                                                                                                                                                                                                              282

Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.eeeeee.hhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeee....hhhhhhh...eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee....hhhhh..eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utn B  33 SSDLTAFREHFAKAKHIAIITGAGVSAESGVPTFRGPGGFWRKWQAQDLATPEAFSRDPSLVWEFYHYRREVMRSKMPNPAHLAIAECEARLGQQGRSVVIITQNIDELHHRAGSKHVYEIHGSLFKTRCMSCGEVKANHKSPICPALDGKGAPDPNTKEARIPVELLPRCERKSCNGLLRPHVVWFGETLDSDILTAVERELEKCDLCLVVGTSSIVYPAAMFAPQVASRGVPVAEFNMECTPATQRFKYHFEGPCGSTLPPALE 298
                                    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

Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ....hhhhh Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4utn D   0 xGVLkEYGV   8
                            |   |    
                            0-BEZ    
                                4-SLL

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 4UTN)

(no "CATH Domain" information available for 4UTN)

(no "Pfam Domain" information available for 4UTN)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ser A:174 - Pro A:175	[ RasMol ]
		Ser B:174 - Pro B:175	[ RasMol ]
		Tyr A:251 - Pro A:252	[ RasMol ]
		Tyr B:251 - Pro B:252	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	SIR5_DANRE \| Q6DHI5	:	4utr 4utv 4utx 4utz 4uu7 4uu8 4uua 4uub

4utr	CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH GLUTARYLATED CPS1-PEPTIDE
4utv	CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3-PHENYL-SUCCINYLATED CPS1-PEPTIDE
4utx	CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3-NITRO-PROPIONYLATED CPS1-PEPTIDE
4utz	CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH ADIPOYLATED CPS1-PEPTIDE
4uu7	CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3-METHYL-SUCCINYLATED CPS1-PEPTIDE
4uu8	CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3,3-DIMETHYL-SUCCINYLATED CPS1-PEPTIDE
4uua	CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3S-Z-AMINO-SUCCINYLATED CPS1-PEPTIDE
4uub	CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 2R-BUTYL-SUCCINYLATED CPS1-PEPTIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 7)

Sites (5, 5)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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