1AFY - JenaLib

Theoretical Model (Jmol Viewer)

Theor. Model - sites (Jmol Viewer)

Title :   THE MODELED STRUCTURE OF THE THIOLASE/ACETOACTYL-COA COMPLEX, THEORETICAL MODEL

Authors :   Y. Modis, C. Engel, R. Abagyan, R. K. Wierenga

Date :   17 Mar 97 (Deposition) - 16 Jun 97 (Release) - 16 Jun 97 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,B,_^#
( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Keywords :   Thiolase, Fatty Acid Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Mathieu, Y. Modis, J. P. Zeelen, C. K. Engel, R. A. Abagyan, A. Ahlberg, B. Rasmussen, V. S. Lamzin, W. H. Kunau, R. K. Wierenga
The 1. 8 Angstroms Crystal Structure Of The Dimeric Peroxisomal Thiolase Of Saccharomyces Cerevisiae: Implications For Substrate Binding And Reaction Mechanism
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - 3-KETOACYL-COA THIOLASE
	Cellular Location	:	PEROXISOME
	Chains	:	A, B
	EC Number	:	2.3.1.16
	Organelle	:	PEROXISOME
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE


Theoretical Model	:

( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Summary Information (see also Sequences/Alignments below)

Theoretical Model (1, 1)

No.	Name	Count	Type	Full Name
1	CAA	1	Ligand/Ion	ACETOACETYL-COENZYME A

Theoretical Model (2, 2)

No.	Name	Evidence	Residues	Description
1	AVA	not defined	CYS A:125 , HIS A:375 , CYS A:403	THE ACETOACETYL-COA MOLECULE IS MODELED INTO THIS ACTIVE SITE.
2	AVB	not defined	CYS B:125 , HIS B:375 , CYS B:403	ACTIVE SITE IN CHAIN B.

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

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

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

Theoretical Model (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOLASE_1	PS00098	Thiolases acyl-enzyme intermediate signature.	THIK_YEAST	121-139	2	A:121-139 B:121-139
2	THIOLASE_2	PS00737	Thiolases signature 2.	THIK_YEAST	365-381	2	A:365-381 B:365-381
3	THIOLASE_3	PS00099	Thiolases active site.	THIK_YEAST	398-411	2	A:398-411 B:398-411

Theoretical Model (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YIL160C	1	YIL160C.1	IX:41444-40191	1254	THIK_YEAST	1-417	417	2	A:25-417 (gaps) B:25-417	393 393

Theoretical Model

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:390
 aligned with THIK_YEAST | P27796 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:393
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
           THIK_YEAST    25 KNSLLEKRPEDVVIVAANRSAIGKGFKGAFKDVNTDYLLYNFLNEFIGRFPEPLRADLNLIEEVACGNVLNVGAGATEHRAACLASGIPYSTPFVALNRQCSSGLTAVNDIANKIKVGQIDIGLALGVESMTNNYKNVNPLGMISSEELQKNREAKKCLIPMGITNENVAANFKISRKDQDEFAANSYQKAYKAKNEGLFEDEILPIKLPDGSICQSDEGPRPNVTAESLSSIRPAFIKDRGTTTAGNASQVSDGVAGVLLARRSVANQLNLPVLGRYIDFQTVGVPPEIMGVGPAYAIPKVLEATGLQVQDIDIFEINEAFAAQALYCIHKLGIDLNKVNPRGGAIALGHPLGCTGARQVATILRELKKDQIGVVSMCIGTGMGAAAIFIKE 417
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh......eeeeeeee.........hhhh..hhhhhhhhhhhhhh...hhhh..hhh...eeee....hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhhhhh....eeeeeeeee................hhhhh...hhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhh.......................hhhhhh......---............eeeeeeeeeehhhhhhh.....eeeeeeeeee..hhhhhhhhhhhhhhhhhhh...hhh..eeee....hhhhhhhhhhh...hhh......hhhh...hhhhhhhhhhhhhhh.....eeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------THIOLASE_1         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOLASE_2       ----------------THIOLASE_3    ------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:25-417 (gaps) UniProt: 1-417 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                Transcript 1
                 1afy A  25 KNSLLEKRPEDVVIVAANRSAIGKGFKGAFKDVNTDYLLYNFLNEFIGRFPEPLRADLNLIEEVACGNVLNVGAGATEHRAACLASGIPYSTPFVALNRQCSSGLTAVNDIANKIKVGQIDIGLALGVESMTNNYKNVNPLGMISSEELQKNREAKKCLIPMGITNENVAANFKISRKDQDEFAANSYQKAYKAKNEGLFEDEILPIKLPDGSICQSDEGPRPNVTAESLSSIRPAFI---GTTTAGNASQVSDGVAGVLLARRSVANQLNLPVLGRYIDFQTVGVPPEIMGVGPAYAIPKVLEATGLQVQDIDIFEINEAFAAQALYCIHKLGIDLNKVNPRGGAIALGHPLGCTGARQVATILRELKKDQIGVVSMCIGTGMGAAAIFIKE 417
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       | - |     274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
                                                                                                                                                                                                                                                                       262 266

Chain B from PDB  Type:PROTEIN  Length:393
 aligned with THIK_YEAST | P27796 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:393
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
           THIK_YEAST    25 KNSLLEKRPEDVVIVAANRSAIGKGFKGAFKDVNTDYLLYNFLNEFIGRFPEPLRADLNLIEEVACGNVLNVGAGATEHRAACLASGIPYSTPFVALNRQCSSGLTAVNDIANKIKVGQIDIGLALGVESMTNNYKNVNPLGMISSEELQKNREAKKCLIPMGITNENVAANFKISRKDQDEFAANSYQKAYKAKNEGLFEDEILPIKLPDGSICQSDEGPRPNVTAESLSSIRPAFIKDRGTTTAGNASQVSDGVAGVLLARRSVANQLNLPVLGRYIDFQTVGVPPEIMGVGPAYAIPKVLEATGLQVQDIDIFEINEAFAAQALYCIHKLGIDLNKVNPRGGAIALGHPLGCTGARQVATILRELKKDQIGVVSMCIGTGMGAAAIFIKE 417
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh......eeeeeeee.........hhhh..hhhhhhhhhhhhhhh..hhhhh.hhh..eeeee....hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhh....eeeeeeeee................hhhhh...hhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.............................hhhhhh.....................eeeeeeeeeehhhhhhh.....eeeeeeeeee..hhhhhhhhhhhhhhhhhhh...hhh..eeee....hhhhhhhhhhh...hhh......hhhh...hhhhhhhhhhhhhhh.....eeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------THIOLASE_1         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOLASE_2       ----------------THIOLASE_3    ------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:25-417 UniProt: 1-417 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                       Transcript 1
                 1afy B  25 KNSLLEKRPEDVVIVAANRSAIGKGFKGAFKDVNTDYLLYNFLNEFIGRFPEPLRADLNLIEEVACGNVLNVGAGATEHRAACLASGIPYSTPFVALNRQCSSGLTAVNDIANKIKVGQIDIGLALGVESMTNNYKNVNPLGMISSEELQKNREAKKCLIPMGITNENVAANFKISRKDQDEFAANSYQKAYKAKNEGLFEDEILPIKLPDGSICQSDEGPRPNVTAESLSSIRPAFIKDRGTTTAGNASQVSDGVAGVLLARRSVANQLNLPVLGRYIDFQTVGVPPEIMGVGPAYAIPKVLEATGLQVQDIDIFEINEAFAAQALYCIHKLGIDLNKVNPRGGAIALGHPLGCTGARQVATILRELKKDQIGVVSMCIGTGMGAAAIFIKE 417
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414

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 1AFY)

(no "CATH Domain" information available for 1AFY)

(no "Pfam Domain" information available for 1AFY)

Theoretical Model(hide GO term definitions)

Chain A,B (THIK_YEAST | P27796)

molecular function
	GO:0003988	acetyl-CoA C-acyltransferase activity	Catalysis of the reaction: acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	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:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
	GO:0016747	transferase activity, transferring acyl groups other than amino-acyl groups	Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
biological process
	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:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005782	peroxisomal matrix	The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
	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.

Theoretical Model
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(no "Cis Peptide Bonds" information available for 1afy)

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	1afy
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	THIK_YEAST \| P27796	:	1afw 1pxt 3w15

(no "Related Entries Specified in the PDB File" available for 1AFY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (1, 2)

Sequences/Alignments

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Gene Ontology (14, 14)

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