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

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

Date :   22 Jul 14 (Deposition) - 20 Aug 14 (Release) - 08 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Hydrolase, Sirtuin 5, Regulatory Enzyme, Deacylase, Mitochondrial, 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
	Fragment	:	CATALYTIC CORE, UNP RESIDUES 30-298
	Organism Common	:	ZEBRAFISH
	Organism Scientific	:	DANIO RERIO
	Organism Taxid	:	7955

Molecule 2 - GLUTARYL-CPS1 PEPTIDE
	Chains	:	C
	Fragment	:	UNP RESIDUES 524-531
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	BENZOYLATED GLYCINE AT PEPTIDE POSITION 1 GLUTARYLATED LYSINE AT PEPTIDE POSITION 4
	Synonym	:	3-NITRO-PROPIONYL-CPS1 PEPTIDE
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 9)

No.	Name	Count	Type	Full Name
1	BEZ	1	Mod. Amino Acid	BENZOIC ACID
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
4	GUA	1	Ligand/Ion	GLUTARIC ACID
5	NA	1	Ligand/Ion	SODIUM ION
6	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	BEZ	1	Mod. Amino Acid	BENZOIC ACID
2	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	GUA	1	Ligand/Ion	GLUTARIC ACID
5	NA	-1	Ligand/Ion	SODIUM ION
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (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	GUA	-1	Ligand/Ion	GLUTARIC ACID
5	NA	-1	Ligand/Ion	SODIUM ION
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:98 , ARG A:101 , VAL A:217 , PHE A:219 , LYS C:4	BINDING SITE FOR RESIDUE GUA C1299
2	AC2	SOFTWARE	CYS B:162 , CYS B:165 , CYS B:203 , CYS B:208	BINDING SITE FOR RESIDUE ZN B1299
3	AC3	SOFTWARE	CYS A:162 , CYS A:165 , CYS A:203 , CYS A:208	BINDING SITE FOR RESIDUE ZN A1300
4	AC4	SOFTWARE	GLN A:136 , ASN A:137 , ILE A:138 , ASP A:139	BINDING SITE FOR RESIDUE EDO A1301
5	AC5	SOFTWARE	GLU B:232 , GLU B:236 , GLN B:259 , ARG B:263	BINDING SITE FOR RESIDUE EDO B1300
6	AC6	SOFTWARE	GLU A:232 , VAL B:217	BINDING SITE FOR RESIDUE EDO A1302
7	AC7	SOFTWARE	ARG A:144 , ALA A:145 , ARG B:144 , ALA B:145 , GLY B:146	BINDING SITE FOR RESIDUE DMS B1301
8	AC8	SOFTWARE	ASP B:224 , ASP B:226	BINDING SITE FOR RESIDUE NA 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 4UTR)

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

(no "Exon" information available for 4UTR)

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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.eeeeee.hhhhhh...........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....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
                 4utr A  35 DLTAFREHFAKAKHIAIITGAGVSAESGVPTFRGPGGFWRKWQAQDLATPEAFSRDPSLVWEFYHYRREVMRSKMPNPAHLAIAECEARLGQQGRSVVIITQNIDELHHRAGSKHVYEIHGSLFKTRCMSCGEVKANHKSPICPALDGKGAPDPNTKEARIPVELLPRCERKSCNGLLRPHVVWFGETLDSDILTAVERELEKCDLCLVVGTSSIVYPAAMFAPQVASRGVPVAEFNMECTPATQKYHFEGPCGSTLPPALE 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    || 286       296  
                                                                                                                                                                                                                                                                              279|                
                                                                                                                                                                                                                                                                               282

Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.eeeeee.hhhhhh...........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee....eeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utr B  35 DLTAFREHFAKAKHIAIITGAGVSAESGVPTFRGPGGFWRKWQAQDLATPEAFSRDPSLVWEFYHYRREVMRSKMPNPAHLAIAECEARLGQQGRSVVIITQNIDELHHRAGSKHVYEIHGSLFKTRCMSCGEVKANHKSPICPALDGKGAPDPNTKEARIPVELLPRCERKSCNGLLRPHVVWFGETLDSDILTAVERELEKCDLCLVVGTSSIVYPAAMFAPQVASRGVPVAEFNMECKYHFEGPCGSTLPPALE 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|      291       
                                                                                                                                                                                                                                                                         274|                
                                                                                                                                                                                                                                                                          282

Chain C 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
                 4utr C   0 xGVLKEYGV   8
                            |        
                            0-BEZ

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 4UTR)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		BEZ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DMS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GUA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC4	[ RasMol ]	+environment [ RasMol ]
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		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	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
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4utr
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		Orientation in Membranes	:	OPM
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Access by UniProt ID/Accession number
	CPSM_HUMAN \| P31327
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	Q5R209_HUMAN \| Q5R209
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	SIR5_DANRE \| Q6DHI5
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.5.1.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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	SIR5_DANRE \| Q6DHI5
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UniProtKB/Swiss-Prot
	CPSM_HUMAN \| P31327	:	2yvq 4utv 4utx 4utz 4uu7 4uu8 4uua 4uub 5dot 5dou
	Q5R209_HUMAN \| Q5R209	:	4utv 4utx 4utz 4uu7 4uu8 4uua 4uub
	SIR5_DANRE \| Q6DHI5	:	4utn 4utv 4utx 4utz 4uu7 4uu8 4uua 4uub

4utn	CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH SUCCINYLATED 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, 9)

Sites (8, 8)

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 (71, 82)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File