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Title :   CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF YEAST PEROXISOMAL THIOESTERASE-1

Authors :   Y. D. Devedjiev, J. Li, U. Derewenda, Z. S. Derewenda

Date :   20 May 04 (Deposition) - 04 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Yeast Peroxisomal Thioesterase; X-Ray Structure; Domain Swapping; Iodine Soak; Siras, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. D. Devedjiev, J. Li, U. Derewenda, Z. S. Derewenda
Crystal Structure Of N-Terminal Domain Of Yeast Peroxisomal Thioesterase-1
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PEROXISOMAL ACYL-COENZYME A THIOESTER HYDROLASE 1
	Chains	:	A, B, C, D
	EC Number	:	3.1.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	PTE1, TES1, YJR019C, J1456
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PEROXISOMAL LONG-CHAIN ACYL-COA THIOESTERASE 1

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FMT	2	Ligand/Ion	FORMIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:64 , SER B:65 , LEU B:113 , GLN C:85 , SER C:99 , THR C:109	BINDING SITE FOR RESIDUE FMT B 200
2	AC2	SOFTWARE	GLN A:97 , LEU A:106 , THR A:109 , THR D:64 , SER D:65 , LEU D:113 , HOH D:214	BINDING SITE FOR RESIDUE FMT D 201

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

(no "Cis Peptide Bond" information available for 1TBU)

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

(no "PROSITE Motif" information available for 1TBU)

Asymmetric/Biological Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YJR019C	1	YJR019C.1	X:468273-467224	1050	PTE1_YEAST	1-349	349	4	A:13-116 (gaps) B:13-118 (gaps) C:14-117 (gaps) D:14-118 (gaps)	104 106 104 105

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
	(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:96
 aligned with PTE1_YEAST | P41903 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:104
                                    22        32        42        52        62        72        82        92       102       112    
           PTE1_YEAST    13 KILELVPLSPTSFVTKYLPAAPVGSKGTFGGTLVSQSLLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFAV 116
               SCOP domains d1tbua1 A:13-116 Pe        roxisomal long-chain acyl-CoA thioesterase 1, TES1                            SCOP domains
               CATH domains 1tbuA00 A:13-116  [        code=3.10.129.10, no name defined]                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee....eeee....--------.hhhhhhhhhhhhhhh......eeeeeeeee..........eeeeeeeee...eeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:13-116 (gaps) UniProt: 1-349 [INCOMPLETE]                                               Transcript 1
                 1tbu A  13 KILELVPLSPTSFVTKYLP--------TFGGTLVSQSLLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFAV 116
                                    22        |-       |42        52        62        72        82        92       102       112    
                                             31       40

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with PTE1_YEAST | P41903 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:106
                                    22        32        42        52        62        72        82        92       102       112      
           PTE1_YEAST    13 KILELVPLSPTSFVTKYLPAAPVGSKGTFGGTLVSQSLLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFAVQR 118
               SCOP domains d1tbub_ B: Peroxis        omal long-chain acyl-CoA thioesterase 1, TES1                                    SCOP domains
               CATH domains 1tbuB00 B:13-118          [code=3.10.129.10, no name defined]                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeee...--------.hhhhhhhhhhhhhhhh.....eeeeeeeeee..........eeeeeeeee...eeeeeeeeee..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:13-118 (gaps) UniProt: 1-349 [INCOMPLETE]                                                 Transcript 1
                 1tbu B  13 KILELVPLSPTSFVTKYL--------GTFGGTLVSQSLLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFAVQR 118
                                    22       | -      | 42        52        62        72        82        92       102       112      
                                            30       39

Chain C from PDB  Type:PROTEIN  Length:96
 aligned with PTE1_YEAST | P41903 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:104
                                    23        33        43        53        63        73        83        93       103       113    
           PTE1_YEAST    14 ILELVPLSPTSFVTKYLPAAPVGSKGTFGGTLVSQSLLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFAVQ 117
               SCOP domains d1tbuc_ C: Peroxis        omal long-chain acyl-CoA thioesterase 1, TES1                                  SCOP domains
               CATH domains 1tbuC00 C:14-117          [code=3.10.129.10, no name defined]                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eeee....--------.hhhhhhhhhhhhhhh.....eeeeeeeeee..........eeeeeeeee...eeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:14-117 (gaps) UniProt: 1-349 [INCOMPLETE]                                               Transcript 1
                 1tbu C  14 ILELVPLSPTSFVTKYLP--------TFGGTLVSQSLLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFAVQ 117
                                    23       | -      | 43        53        63        73        83        93       103       113    
                                            31       40

Chain D from PDB  Type:PROTEIN  Length:97
 aligned with PTE1_YEAST | P41903 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:105
                                    23        33        43        53        63        73        83        93       103       113     
           PTE1_YEAST    14 ILELVPLSPTSFVTKYLPAAPVGSKGTFGGTLVSQSLLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFAVQR 118
               SCOP domains d1tbud_ D: Peroxi        somal long-chain acyl-CoA thioesterase 1, TES1                                   SCOP domains
               CATH domains 1tbuD00 D:14-118          [code=3.10.129.10, no name defined]                                             CATH domains
           Pfam domains (1) ------Acyl_CoA_th        io-1tbuD01 D:20-118                                                              Pfam domains (1)
           Pfam domains (2) ------Acyl_CoA_th        io-1tbuD02 D:20-118                                                              Pfam domains (2)
           Pfam domains (3) ------Acyl_CoA_th        io-1tbuD03 D:20-118                                                              Pfam domains (3)
           Pfam domains (4) ------Acyl_CoA_th        io-1tbuD04 D:20-118                                                              Pfam domains (4)
         Sec.struct. author ...eee....eeee...--------hhhhhhhhhhhhhhhhh.....eeeeeeeeee..........eeeeee......eeeeeeeeee..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:14-118 (gaps) UniProt: 1-349 [INCOMPLETE]                                                Transcript 1
                 1tbu D  14 ILELVPLSPTSFVTKYL--------GTFGGTLVSQSLLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFAVQR 118
                                    23      |  -     |  43        53        63        73        83        93       103       113     
                                           30       39

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Thioesterase/thiol ester dehydrase-isomerase (151)

Superfamily: Thioesterase/thiol ester dehydrase-isomerase (151)

Family: Acyl-CoA thioesterase (2)

Protein domain: Peroxisomal long-chain acyl-CoA thioesterase 1, TES1 (1)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (1)

1a	d1tbua1	A:13-116
1b	d1tbub_	B:
1c	d1tbuc_	C:
1d	d1tbud_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Thiol Ester Dehydrase; Chain A (90)

Homologous Superfamily: [code=3.10.129.10, no name defined] (90)

Baker's yeast (Saccharomyces cerevisiae) (1)

1a	1tbuB00	B:13-118
1b	1tbuD00	D:14-118
1c	1tbuA00	A:13-116
1d	1tbuC00	C:14-117

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HotDog (52)

Family: Acyl_CoA_thio (1)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (1)

1a	Acyl_CoA_thio-1tbuD01	D:20-118
1b	Acyl_CoA_thio-1tbuD02	D:20-118
1c	Acyl_CoA_thio-1tbuD03	D:20-118
1d	Acyl_CoA_thio-1tbuD04	D:20-118

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (PTE1_YEAST | P41903)

molecular function
	GO:0047617	acyl-CoA hydrolase activity	Catalysis of the reaction: acyl-CoA + H2O = CoA + a carboxylate.
	GO:0052689	carboxylic ester hydrolase activity	Catalysis of the hydrolysis of a carboxylic ester bond.
	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:0016290	palmitoyl-CoA hydrolase activity	Catalysis of the reaction: palmitoyl-CoA + H2O = CoA + palmitate.
biological process
	GO:0006637	acyl-CoA metabolic process	The chemical reactions and pathways involving acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with an acyl group.
	GO:0006635	fatty acid beta-oxidation	A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
	GO:0019395	fatty acid oxidation	The removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydrogen.
cellular component
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

Asymmetric/Biological Unit
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1c8u	BACTERIAL ISOFORM OF THE SAME ENZYME

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Ligands, Modified Residues, Ions (1, 2)

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