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Description

Title :   CRYSTAL STRUCTURE OF RAT MITOCHONDRIAL 3,2-ENOYL-COA

Authors :   P. A. Hubbard, W. Yu, H. Schulz, J. -J. Kim

Date :   03 Nov 04 (Deposition) - 23 Nov 04 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)
Biol. Unit 2: A  (2x)

Keywords :   Crotonase Superfamily, Domain Swapped, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. A. Hubbard, W. Yu, H. Schulz, J. J. Kim
Domain Swapping In The Low-Similarity Isomerase/Hydratase Superfamily: The Crystal Structure Of Rat Mitochondrial Delta3, Delta2-Enoyl-Coa Isomerase.
Protein Sci. V. 14 1545 2005
PubMed-ID: 15883186 | Reference-DOI: 10.1110/PS.041303705

Compounds

Molecule 1 - 3,2-TRANS-ENOYL-COA ISOMERASE, MITOCHONDRIAL
	Chains	:	A
	EC Number	:	5.3.3.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PND-1
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DCI
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	DODECENOYL-COA DELTA-ISOMERASE

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 9)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	BAM	3	Ligand/Ion	BENZAMIDINE
2	PO4	3	Ligand/Ion	PHOSPHATE ION
3	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	BAM	9	Ligand/Ion	BENZAMIDINE
2	PO4	9	Ligand/Ion	PHOSPHATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	BAM	6	Ligand/Ion	BENZAMIDINE
2	PO4	6	Ligand/Ion	PHOSPHATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:59 , ARG A:103 , ASN A:104 , HIS A:107 , GLU A:110 , ZN A:400 , HOH A:518	BINDING SITE FOR RESIDUE PO4 A 300
2	AC2	SOFTWARE	HIS A:220 , HIS A:278 , GLU A:282 , PO4 A:302 , ZN A:401 , ZN A:402	BINDING SITE FOR RESIDUE PO4 A 301
3	AC3	SOFTWARE	HIS A:220 , ARG A:224 , HIS A:278 , PO4 A:301 , ZN A:401 , ZN A:402	BINDING SITE FOR RESIDUE PO4 A 302
4	AC4	SOFTWARE	HIS A:107 , GLU A:110 , PO4 A:300	BINDING SITE FOR RESIDUE ZN A 400
5	AC5	SOFTWARE	HIS A:220 , PO4 A:301 , PO4 A:302 , ZN A:402	BINDING SITE FOR RESIDUE ZN A 401
6	AC6	SOFTWARE	HIS A:278 , PO4 A:301 , PO4 A:302 , ZN A:401	BINDING SITE FOR RESIDUE ZN A 402
7	AC7	SOFTWARE	VAL A:171 , PHE A:267	BINDING SITE FOR RESIDUE BAM A 600
8	AC8	SOFTWARE	TRP A:112 , VAL A:171 , PRO A:173 , ASP A:260 , PHE A:267 , HOH A:510 , HOH A:573	BINDING SITE FOR RESIDUE BAM A 700
9	AC9	SOFTWARE	ILE A:170 , VAL A:171 , PHE A:264 , PHE A:267	BINDING SITE FOR RESIDUE BAM A 800

SS Bonds (0, 0)

(no "SS Bond" information available for 1XX4)

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Pro A:52	-	Pro A:53

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1XX4)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOYL_COA_HYDRATASE	PS00166	Enoyl-CoA hydratase/isomerase signature.	ECI1_RAT	130-150	1	A:130-150

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOYL_COA_HYDRATASE	PS00166	Enoyl-CoA hydratase/isomerase signature.	ECI1_RAT	130-150	3	A:130-150

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOYL_COA_HYDRATASE	PS00166	Enoyl-CoA hydratase/isomerase signature.	ECI1_RAT	130-150	2	A:130-150

Exons (0, 0)

(no "Exon" information available for 1XX4)

Sequences/Alignments

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:254
 aligned with ECI1_RAT | P23965 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:257
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       
             ECI1_RAT    29 FSNKRVLVEKEGEAGIAVMKFKNPPVNSLSLEFLTEFVISLEKLENDKSIRGVILTSERPGIFSAGLDLMEMYGRNPAHYAEYWKAVQELWLRLYLSNLTLISAINGASPAGGCLMALTCDYRIMADNSKYTIGLNESLLGIVAPFWLKDNYVNTIGHRAAERALQLGTLFPPAEALKVGLVDEVVPEDQVHSKARSVMAKWFTIPDHSRQLTKSMMRKATADNLIKQREADIQNFTSFISRDSIQKSLHVYLEKLK 285
               SCOP domains d1xx4a_ A:    Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomerase)                                                                                                                                                                                           SCOP domains
               CATH domains 1xx4A01 A:   29-233 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                 ---------------------------------------------------- CATH domains
               Pfam domains --------EC   H-1xx4A01 A:37-283                                                                                                                                                                                                                                -- Pfam domains
         Sec.struct. author .....eeee.---..eeeeee......eehhhhhhhhhhhhhhhhhh....eeeeee...ee...ee.hhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeee.eeeehhhhhhhhhh.eeeee......ee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh....eeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xx4 A  29 FSNKRVLVEK---AGIAVMKFKNPPVNSLSLEFLTEFVISLEKLENDKSIRGVILTSERPGIFSAGLDLMEMYGRNPAHYAEYWKAVQELWLRLYLSNLTLISAINGASPAGGCLMALTCDYRIMADNSKYTIGLNESLLGIVAPFWLKDNYVNTIGHRAAERALQLGTLFPPAEALKVGLVDEVVPEDQVHSKARSVMAKWFTIPDHSRQLTKSMMRKATADNLIKQREADIQNFTSFISRDSIQKSLHVYLEKLK 285
                                    38   |    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       
                                    38  42

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: ClpP/crotonase (207)

Superfamily: ClpP/crotonase (207)

Family: Crotonase-like (39)

Protein domain: Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomerase) (8)

Norway rat (Rattus norvegicus), mitochondrial [TaxId: 10116] (1)

d1xx4a_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: 2-enoyl-CoA Hydratase; Chain A, domain 1 (89)

Homologous Superfamily: 2-enoyl-CoA Hydratase; Chain A, domain 1 (89)

Norway rat (Rattus norvegicus) (6)

1xx4A01

A:29-233

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ClpP_crotonase (88)

Family: ECH (52)

Rattus norvegicus (Rat) (3)

ECH-1xx4A01

A:37-283

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (ECI1_RAT | P23965)

molecular function
	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:0004165	dodecenoyl-CoA delta-isomerase activity	Catalysis of the reaction: 3-cis-dodecenoyl-CoA = 2-trans-dodecenoyl-CoA.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
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: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: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.

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Related Entries

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Related Entries Specified in the PDB File

1dub	CRYSTAL STRUCTURE OF CROTONASE
1hzd	CRYSTAL STRUCTURE OF HUMAN AUH PROTEIN
1pjh	CRYSTAL STRUCTURE OF PEROXISOMAL 3,2-ENOYOL-COA ISOMERASE