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Title :   CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3-NITRO-PROPIONYLATED CPS1-PEPTIDE

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

Date :   23 Jul 14 (Deposition) - 20 Aug 14 (Release) - 08 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Hydrolase, 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
	Synonym	:	SIRTUIN 5, REGULATORY PROTEIN SIR2 HOMOLOG 5

Molecule 2 - CARBAMOYLPHOSPHATE SYNTHETASE I
	Chains	:	C
	Fragment	:	UNP RESIDUES 524-531
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	BENZOYLATED GLYCINE AT POSITION 1. 3-NITRO- PROPIONYLATED LYSINE AT 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 (7, 10)

No.	Name	Count	Type	Full Name
1	3NP	1	Ligand/Ion	3-NITROPROPANOIC ACID
2	BEZ	1	Mod. Amino Acid	BENZOIC ACID
3	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
4	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
5	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
6	NA	1	Ligand/Ion	SODIUM ION
7	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	3NP	1	Ligand/Ion	3-NITROPROPANOIC ACID
2	BEZ	1	Mod. Amino Acid	BENZOIC ACID
3	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
4	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
5	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
6	NA	-1	Ligand/Ion	SODIUM ION
7	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	3NP	-1	Ligand/Ion	3-NITROPROPANOIC ACID
2	BEZ	-1	Mod. Amino Acid	BENZOIC ACID
3	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
4	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
5	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
6	NA	-1	Ligand/Ion	SODIUM ION
7	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:67 , TYR A:98 , ARG A:101 , VAL A:216 , VAL A:217 , PHE A:219 , EDO A:1300 , LYS C:4	BINDING SITE FOR RESIDUE 3NP C1004
2	AC2	SOFTWARE	CYS A:162 , CYS A:165 , CYS A:203 , CYS A:208	BINDING SITE FOR RESIDUE ZN A1299
3	AC3	SOFTWARE	CYS B:162 , CYS B:165 , CYS B:203 , CYS B:208	BINDING SITE FOR RESIDUE ZN B1299
4	AC4	SOFTWARE	THR A:229 , GLU A:232 , ALA B:78 , ALA B:82 , TYR B:98 , ARG B:101 , HIS B:154 , VAL B:217 , TRP B:218 , PHE B:219 , GLU B:221 , TYR B:251	BINDING SITE FOR RESIDUE EPE B1300
5	AC5	SOFTWARE	ARG B:144 , ALA B:145 , GLY B:146 , HOH B:2011	BINDING SITE FOR RESIDUE DMS B1301
6	AC6	SOFTWARE	GLN A:136 , ASN A:137 , HIS A:154 , 3NP C:1004	BINDING SITE FOR RESIDUE EDO A1300
7	AC7	SOFTWARE	GLY A:245 , ASN A:271 , MET A:272 , GLU A:273	BINDING SITE FOR RESIDUE EDO A1301
8	AC8	SOFTWARE	ASN B:137 , ILE B:138 , ASP B:139	BINDING SITE FOR RESIDUE EDO B1302
9	AC9	SOFTWARE	ASP B:224 , ASP B:226	BINDING SITE FOR RESIDUE NA B1303

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 4UTX)

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

(no "Exon" information available for 4UTX)

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.eeeeeehhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..eeeeee....hhhhhh....eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhh....eeeee.........eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utx 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.eeeeeehhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..eeeeee....hhhhhh....eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhh....eeeee.....eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4utx B  33 SSDLTAFREHFAKAKHIAIITGAGVSAESGVPTFRGPGGFWRKWQAQDLATPEAFSRDPSLVWEFYHYRREVMRSKMPNPAHLAIAECEARLGQQGRSVVIITQNIDELHHRAGSKHVYEIHGSLFKTRCMSCGEVKANHKSPICPALDGKGAPDPNTKEARIPVELLPRCERKSCNGLLRPHVVWFGETLDSDILTAVERELEKCDLCLVVGTSSIVYPAAMFAPQVASRGVPVAEFNMECFKYHFEGPCGSTLPPALE 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 ||    288       298
                                                                                                                                                                                                                                                                           274|                 
                                                                                                                                                                                                                                                                            281

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
                 4utx 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 4UTX)

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

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

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 ]

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	CPSM_HUMAN \| P31327	:	2yvq 4utr 4utv 4utz 4uu7 4uu8 4uua 4uub 5dot 5dou
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4utn	CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH SUCCINYLATED CPS1-PEPTIDE
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
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 (7, 10)

Sites (9, 9)

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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