1JQI - JenaLib

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Title :   CRYSTAL STRUCTURE OF RAT SHORT CHAIN ACYL-COA DEHYDROGENASE COMPLEXED WITH ACETOACETYL-COA

Authors :   K. P. Battaile, J. Molin-Case, R. Paschke, M. Wang, D. Bennett, J. Vockl J. P. Kim

Date :   07 Aug 01 (Deposition) - 13 Feb 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Flavoprotein, Enzyme-Inhibitor Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. P. Battaile, J. Molin-Case, R. Paschke, M. Wang, D. Bennett, J. Vockley, J. J. Kim
Crystal Structure Of Rat Short Chain Acyl-Coa Dehydrogenase Complexed With Acetoacetyl-Coa: Comparison With Other Acyl-Coa Dehydrogenases.
J. Biol. Chem. V. 277 12200 2002
PubMed-ID: 11812788 | Reference-DOI: 10.1074/JBC.M111296200

Molecule 1 - SHORT CHAIN ACYL-COA DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.3.99.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK-223-3
	Expression System Strain	:	XL1-BLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CAA	2	Ligand/Ion	ACETOACETYL-COENZYME A
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CAA	4	Ligand/Ion	ACETOACETYL-COENZYME A
2	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:94 , LEU A:98 , GLY A:136 , SER A:137 , ALA A:139 , ASN A:183 , PHE A:237 , MET A:241 , GLN A:242 , LEU A:244 , ASP A:245 , ARG A:248 , THR A:318 , TYR A:367 , GLU A:368 , GLY A:369 , FAD A:399 , HOH A:1018 , HOH A:1023 , HOH A:1219 , HOH A:1257	BINDING SITE FOR RESIDUE CAA A 400
2	AC2	SOFTWARE	VAL B:494 , LEU B:498 , GLY B:536 , SER B:537 , ALA B:539 , ASN B:583 , PHE B:637 , MET B:641 , GLN B:642 , LEU B:644 , ASP B:645 , ARG B:648 , THR B:718 , TYR B:767 , GLU B:768 , GLY B:769 , FAD B:799 , HOH B:1067 , HOH B:1089 , HOH B:1133 , HOH B:1135 , HOH B:1178 , HOH B:1204	BINDING SITE FOR RESIDUE CAA B 800
3	AC3	SOFTWARE	PHE A:128 , LEU A:130 , SER A:131 , GLY A:136 , SER A:137 , TRP A:161 , THR A:163 , GLN A:284 , ILE A:363 , THR A:370 , GLU A:372 , LEU A:376 , CAA A:400 , HOH A:1024 , HOH A:1026 , HOH A:1032 , HOH A:1074 , HOH A:1103 , ARG B:673 , PHE B:676 , LEU B:680 , LEU B:683 , GLN B:741 , ILE B:742 , GLY B:745 , HOH B:1004	BINDING SITE FOR RESIDUE FAD A 399
4	AC4	SOFTWARE	ARG A:273 , PHE A:276 , LEU A:283 , GLN A:341 , ILE A:342 , GLY A:345 , HOH A:1027 , PHE B:528 , LEU B:530 , SER B:531 , GLY B:536 , SER B:537 , TRP B:561 , THR B:563 , GLN B:684 , ILE B:763 , THR B:770 , GLU B:772 , LEU B:776 , CAA B:800 , HOH B:1002 , HOH B:1011 , HOH B:1054 , HOH B:1060 , HOH B:1072	BINDING SITE FOR RESIDUE FAD B 799

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

Asymmetric Unit

No.	Residues
1	Met A:193	-	Pro A:194
2	Met B:593	-	Pro B:594

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACYL_COA_DH_1	PS00072	Acyl-CoA dehydrogenases signature 1.	ACADS_RAT	153-165	2	A:129-141 B:529-541
2	ACYL_COA_DH_2	PS00073	Acyl-CoA dehydrogenases signature 2.	ACADS_RAT	365-384	2	A:341-360 B:741-760

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACYL_COA_DH_1	PS00072	Acyl-CoA dehydrogenases signature 1.	ACADS_RAT	153-165	4	A:129-141 B:529-541
2	ACYL_COA_DH_2	PS00073	Acyl-CoA dehydrogenases signature 2.	ACADS_RAT	365-384	4	A:341-360 B:741-760

(no "Exon" information available for 1JQI)

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:384
 aligned with ACADS_RAT | P15651 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:384
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407    
            ACADS_RAT    28 VYQSVELPETHQMLRQTCRDFAEKELVPIAAQLDKEHLFPTSQVKKMGELGLLAMDVPEELSGAGLDYLAYSIALEEISRGCASTGVIMSVNNSLYLGPILKFGSSQQKQQWITPFTNGDKIGCFALSEPGNGSDAGAASTTAREEGDSWVLNGTKAWITNSWEASATVVFASTDRSRQNKGISAFLVPMPTPGLTLGKKEDKLGIRASSTANLIFEDCRIPKENLLGEPGMGFKIAMQTLDMGRIGIASQALGIAQASLDCAVKYAENRHAFGAPLTKLQNIQFKLADMALALESARLLTWRAAMLKDNKKPFTKESAMAKLAASEAATAISHQAIQILGGMGYVTEMPAERYYRDARITEIYEGTSEIQRLVIAGHLLRSYR 411
               SCOP domains d1jqia2 A:4-234 Butyryl-CoA dehydrogenase, NM domains                                                                                                                                                                                  d1jqia1 A:235-387 Butyryl-CoA dehydrogenase, C-domain                                                                                                     SCOP domains
               CATH domains --1jqiA01 A:6-125 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                          1jqiA02 A:126-243 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                                      1jqiA03 A:244-384 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                             --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhh......hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee...............eeee...eeeeeeeeeeee......eeeeeee.hhhhhhh.eeeeeee.....eee.............eeeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------ACYL_COA_DH_1-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACYL_COA_DH_2       --------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jqi A   4 VYQSVELPETHQMLRQTCRDFAEKELVPIAAQLDKEHLFPTSQVKKMGELGLLAMDVPEELSGAGLDYLAYSIALEEISRGCASTGVIMSVNNSLYLGPILKFGSSQQKQQWITPFTNGDKIGCFALSEPGNGSDAGAASTTAREEGDSWVLNGTKAWITNSWEASATVVFASTDRSRQNKGISAFLVPMPTPGLTLGKKEDKLGIRASSTANLIFEDCRIPKENLLGEPGMGFKIAMQTLDMGRIGIASQALGIAQASLDCAVKYAENRHAFGAPLTKLQNIQFKLADMALALESARLLTWRAAMLKDNKKPFTKESAMAKLAASEAATAISHQAIQILGGMGYVTEMPAERYYRDARITEIYEGTSEIQRLVIAGHLLRSYR 387
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383

Chain B from PDB  Type:PROTEIN  Length:384
 aligned with ACADS_RAT | P15651 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:384
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407    
            ACADS_RAT    28 VYQSVELPETHQMLRQTCRDFAEKELVPIAAQLDKEHLFPTSQVKKMGELGLLAMDVPEELSGAGLDYLAYSIALEEISRGCASTGVIMSVNNSLYLGPILKFGSSQQKQQWITPFTNGDKIGCFALSEPGNGSDAGAASTTAREEGDSWVLNGTKAWITNSWEASATVVFASTDRSRQNKGISAFLVPMPTPGLTLGKKEDKLGIRASSTANLIFEDCRIPKENLLGEPGMGFKIAMQTLDMGRIGIASQALGIAQASLDCAVKYAENRHAFGAPLTKLQNIQFKLADMALALESARLLTWRAAMLKDNKKPFTKESAMAKLAASEAATAISHQAIQILGGMGYVTEMPAERYYRDARITEIYEGTSEIQRLVIAGHLLRSYR 411
               SCOP domains d1jqib2 B:404-634 Butyryl-CoA dehydrogenase, NM domains                                                                                                                                                                                d1jqib1 B:635-787 Butyryl-CoA dehydrogenase, C-domain                                                                                                     SCOP domains
               CATH domains --1jqiB01 B:406-525 Butyryl-Coa Dehydrogenase, subunit A, domain 1                                                        1jqiB02 B:526-643 Butyryl-CoA Dehydrogenase, subunit A, domain 2                                                      1jqiB03 B:644-784 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                             --- CATH domains
           Pfam domains (1) -------Acyl-CoA_dh_N-1jqiB05 B:411-523                                                                                  ---Acyl-CoA_dh_M-1jqiB03 B:527-578                     -------------------------------------------------------Acyl-CoA_dh_1-1jqiB01 B:634-783                                                                                                                       ---- Pfam domains (1)
           Pfam domains (2) -------Acyl-CoA_dh_N-1jqiB06 B:411-523                                                                                  ---Acyl-CoA_dh_M-1jqiB04 B:527-578                     -------------------------------------------------------Acyl-CoA_dh_1-1jqiB02 B:634-783                                                                                                                       ---- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhh......hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee........hhhhh..eeee...eeeeeeeeeeee......eeeeeee.hhhhhhh.eeeeeee.....eee.............eeeeeeeeeeee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------ACYL_COA_DH_1-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACYL_COA_DH_2       --------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jqi B 404 VYQSVELPETHQMLRQTCRDFAEKELVPIAAQLDKEHLFPTSQVKKMGELGLLAMDVPEELSGAGLDYLAYSIALEEISRGCASTGVIMSVNNSLYLGPILKFGSSQQKQQWITPFTNGDKIGCFALSEPGNGSDAGAASTTAREEGDSWVLNGTKAWITNSWEASATVVFASTDRSRQNKGISAFLVPMPTPGLTLGKKEDKLGIRASSTANLIFEDCRIPKENLLGEPGMGFKIAMQTLDMGRIGIASQALGIAQASLDCAVKYAENRHAFGAPLTKLQNIQFKLADMALALESARLLTWRAAMLKDNKKPFTKESAMAKLAASEAATAISHQAIQILGGMGYVTEMPAERYYRDARITEIYEGTSEIQRLVIAGHLLRSYR 787
                                   413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783

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 Unit(hide GO term definitions)

Chain A,B (ACADS_RAT | P15651)

molecular function
	GO:0003995	acyl-CoA dehydrogenase activity	Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor.
	GO:0004085	butyryl-CoA dehydrogenase activity	Catalysis of the reaction: butanoyl-CoA + electron-transfer flavoprotein = 2-butenoyl-CoA + reduced electron-transfer flavoprotein.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0000062	fatty-acyl-CoA binding	Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
	GO:0046359	butyrate catabolic process	The chemical reactions and pathways resulting in the breakdown of butyrate, the anion of butyric acid.
	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:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase	A fatty acid beta-oxidation pathway in which the initial step of each oxidation cycle, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA dehydrogenase; the electrons removed by oxidation pass through the respiratory chain to oxygen and leave H2O as the product. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when 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:0055088	lipid homeostasis	Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
	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.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0051384	response to glucocorticoid	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
	GO:0042594	response to starvation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
cellular component
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0031966	mitochondrial membrane	Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric Unit
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	Cis Peptide Bonds
		Met A:193 - Pro A:194	[ RasMol ]
		Met B:593 - Pro B:594	[ RasMol ]

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	1jqi
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