1UUM - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   RAT DIHYDROOROTATE DEHYDROGENASE (DHOD)IN COMPLEX WITH ATOVAQUONE

Authors :   M. Hansen, J. Le Nours, E. Johansson, T. Antal, A. Ullrich, M. Loffler, S. Larsen

Date :   06 Jan 04 (Deposition) - 01 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Oxidoreductase, Dihydroorotate Dehydrogenase, Brequinar, Atovaquone, Nucleotide Metabolism, Pyrimidine Biosynthesis, Fad, Flavoprotein, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hansen, J. Le Nours, E. Johansson, T. Antal, A. Ullrich, M. Loffler, S. Larsen
Inhibitor Binding In A Class 2 Dihydroorotate Dehydrogenase Causes Variations In The Membrane-Associated N-Terminal Domain
Protein Sci. V. 13 1031 2004
PubMed-ID: 15044733 | Reference-DOI: 10.1110/PS.03533004

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.3.99.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BLACK RAT, ROOF RAT
	Organism Scientific	:	RATTUS RATTUS
	Organism Taxid	:	10117
	Synonym	:	MITOCHONDRIAL PRECURSOR, DIHYDROOROTATE OXIDASE, DHODEHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	AFI	2	Ligand/Ion	2-[4-(4-CHLOROPHENYL)CYCLOHEXYLIDENE]-3,4-DIHYDROXY-1(2H)-NAPHTHALENONE
2	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE
3	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
4	ORO	2	Ligand/Ion	OROTIC ACID

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	AFI	1	Ligand/Ion	2-[4-(4-CHLOROPHENYL)CYCLOHEXYLIDENE]-3,4-DIHYDROXY-1(2H)-NAPHTHALENONE
2	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE
3	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
4	ORO	1	Ligand/Ion	OROTIC ACID

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	AFI	1	Ligand/Ion	2-[4-(4-CHLOROPHENYL)CYCLOHEXYLIDENE]-3,4-DIHYDROXY-1(2H)-NAPHTHALENONE
2	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE
3	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
4	ORO	1	Ligand/Ion	OROTIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:46 , LEU A:50 , ASP A:51 , SER A:54 , ARG A:61 , ARG A:131 , HOH A:2099	BINDING SITE FOR RESIDUE BOG A 401
2	AC2	SOFTWARE	LEU B:50 , ASP B:51 , SER B:54 , ARG B:61 , ARG B:131 , HOH B:2106	BINDING SITE FOR RESIDUE BOG B 401
3	AC3	SOFTWARE	ALA A:95 , ALA A:96 , GLY A:97 , LYS A:100 , SER A:120 , ASN A:145 , ASN A:181 , ASN A:212 , LYS A:255 , THR A:283 , ASN A:284 , THR A:285 , SER A:305 , GLY A:306 , LEU A:309 , VAL A:333 , GLY A:334 , GLY A:335 , LEU A:355 , TYR A:356 , THR A:357 , ORO A:399 , AFI A:400 , HOH A:2096 , HOH A:2097	BINDING SITE FOR RESIDUE FMN A 398
4	AC4	SOFTWARE	LYS A:100 , ASN A:145 , TYR A:147 , GLY A:148 , PHE A:149 , ASN A:212 , SER A:215 , ASN A:284 , THR A:285 , FMN A:398 , HOH A:2098	BINDING SITE FOR RESIDUE ORO A 399
5	AC5	SOFTWARE	GLU A:40 , MET A:43 , PRO A:44 , GLN A:47 , PRO A:52 , ALA A:55 , HIS A:56 , ALA A:59 , PHE A:98 , ARG A:136 , TYR A:356 , LEU A:359 , ILE A:360 , PRO A:364 , FMN A:398	BINDING SITE FOR RESIDUE AFI A 400
6	AC6	SOFTWARE	ALA B:95 , ALA B:96 , GLY B:97 , LYS B:100 , SER B:120 , ASN B:145 , TYR B:147 , ASN B:181 , ASN B:212 , LYS B:255 , THR B:283 , ASN B:284 , THR B:285 , SER B:305 , GLY B:306 , LEU B:309 , VAL B:333 , GLY B:334 , GLY B:335 , LEU B:355 , TYR B:356 , THR B:357 , ORO B:399 , AFI B:400 , HOH B:2037 , HOH B:2103 , HOH B:2104	BINDING SITE FOR RESIDUE FMN B 398
7	AC7	SOFTWARE	LYS B:100 , ASN B:145 , TYR B:147 , GLY B:148 , PHE B:149 , ASN B:212 , SER B:215 , ASN B:284 , THR B:285 , FMN B:398 , HOH B:2105	BINDING SITE FOR RESIDUE ORO B 399
8	AC8	SOFTWARE	GLU B:40 , MET B:43 , GLN B:47 , PRO B:52 , ALA B:55 , HIS B:56 , ALA B:59 , PHE B:98 , ARG B:136 , TYR B:356 , LEU B:359 , ILE B:360 , PRO B:364 , FMN B:398	BINDING SITE FOR RESIDUE AFI B 400

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

Asymmetric Unit

No.	Residues
1	Arg A:131	-	Pro A:132
2	Arg B:131	-	Pro B:132

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHODEHASE_1	PS00911	Dihydroorotate dehydrogenase signature 1.	PYRD_RAT	113-132	2	A:114-133 B:114-133
2	DHODEHASE_2	PS00912	Dihydroorotate dehydrogenase signature 2.	PYRD_RAT	329-349	2	A:330-350 B:330-350

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHODEHASE_1	PS00911	Dihydroorotate dehydrogenase signature 1.	PYRD_RAT	113-132	1	A:114-133 -
2	DHODEHASE_2	PS00912	Dihydroorotate dehydrogenase signature 2.	PYRD_RAT	329-349	1	A:330-350 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHODEHASE_1	PS00911	Dihydroorotate dehydrogenase signature 1.	PYRD_RAT	113-132	1	- B:114-133
2	DHODEHASE_2	PS00912	Dihydroorotate dehydrogenase signature 2.	PYRD_RAT	329-349	1	- B:330-350

(no "Exon" information available for 1UUM)

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:350
 aligned with PYRD_RAT | Q63707 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:359
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386         
             PYRD_RAT    37 YAEYLMPGLQRLLDPESAHRLAVRVTSLGLLPRATFQDSDMLEVKVLGHKFRNPVGIAAGFDKNGEAVDGLYKLGFGFVEVGSVTPQPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAQLTADGLPLGINLGKNKTSEDAAADYAEGVRTLGPLADYLVVNVSSPNTAGLRSLQGKTELRHLLSKVLQERDALKGTRKPAVLVKIAPDLTAQDKEDIASVARELGIDGLIVTNTTVSRPVGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRIPIIGVGGVSSGQDALEKIQAGASLVQLYTALIFLGPPVVVRVKRELEALLKERGFTTVTDAIGADHRR 395
               SCOP domains d1uuma_ A: Dihydroorotate dehydrogenase                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1uumA00 A:38-396 Aldolase class I                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhheee..eee...eee.........hhhhhhhh...eeeeeee............eeeehhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh.eeeee...---------.hhhhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhh..eeee............hhhhhh..eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------DHODEHASE_1         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DHODEHASE_2          ---------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uum A  38 YAEYLMPGLQRLLDPESAHRLAVRVTSLGLLPRATFQDSDMLEVKVLGHKFRNPVGIAAGFDKNGEAVDGLYKLGFGFVEVGSVTPQPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAQLTADGLPLGINLGKNKTSEDAAADYAEGVRTLGPLADYLVVNVSS---------QGKTELRHLLSKVLQERDALKGTRKPAVLVKIAPDLTAQDKEDIASVARELGIDGLIVTNTTVSRPVGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRIPIIGVGGVSSGQDALEKIQAGASLVQLYTALIFLGPPVVVRVKRELEALLKERGFTTVTDAIGADHRR 396
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       | -       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387         
                                                                                                                                                                                                           215       225

Chain B from PDB  Type:PROTEIN  Length:350
 aligned with PYRD_RAT | Q63707 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:359
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386         
             PYRD_RAT    37 YAEYLMPGLQRLLDPESAHRLAVRVTSLGLLPRATFQDSDMLEVKVLGHKFRNPVGIAAGFDKNGEAVDGLYKLGFGFVEVGSVTPQPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAQLTADGLPLGINLGKNKTSEDAAADYAEGVRTLGPLADYLVVNVSSPNTAGLRSLQGKTELRHLLSKVLQERDALKGTRKPAVLVKIAPDLTAQDKEDIASVARELGIDGLIVTNTTVSRPVGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRIPIIGVGGVSSGQDALEKIQAGASLVQLYTALIFLGPPVVVRVKRELEALLKERGFTTVTDAIGADHRR 395
               SCOP domains d1uumb_ B: Dihydroorotate dehydrogenase                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1uumB00 B:38-396 Aldolase class I                                                                                                                                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) ----------------------------------------DHO_dh-1uumB01 B:78-378                                                                                                                                                                                                                                                                                      ------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------------DHO_dh-1uumB02 B:78-378                                                                                                                                                                                                                                                                                      ------------------ Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhheee..eee...eee.........hhhhhhhh...eeeeeee............eeeehhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh.eeeee...---------.hhhhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhh..eeee............hhhhhh..eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------DHODEHASE_1         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DHODEHASE_2          ---------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uum B  38 YAEYLMPGLQRLLDPESAHRLAVRVTSLGLLPRATFQDSDMLEVKVLGHKFRNPVGIAAGFDKNGEAVDGLYKLGFGFVEVGSVTPQPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAQLTADGLPLGINLGKNKTSEDAAADYAEGVRTLGPLADYLVVNVSS---------QGKTELRHLLSKVLQERDALKGTRKPAVLVKIAPDLTAQDKEDIASVARELGIDGLIVTNTTVSRPVGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRIPIIGVGGVSSGQDALEKIQAGASLVQLYTALIFLGPPVVVRVKRELEALLKERGFTTVTDAIGADHRR 396
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       | -       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387         
                                                                                                                                                                                                           215       225

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	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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: FMN-linked oxidoreductases (290)

Family: FMN-linked oxidoreductases (242)

Protein domain: Dihydroorotate dehydrogenase (90)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

1a	d1uuma_	A:
1b	d1uumb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Black rat, roof rat (Rattus rattus) (2)

1a	1uumA00	A:38-396
1b	1uumB00	B:38-396

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: DHO_dh (22)

Rattus norvegicus (Rat) (2)

1a	DHO_dh-1uumB01	B:78-378
1b	DHO_dh-1uumB02	B:78-378

Asymmetric Unit(hide GO term definitions)

Chain A,B (PYRD_RAT | Q63707)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	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:0004152	dihydroorotate dehydrogenase activity	Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate.
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	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.
	GO:0048039	ubiquinone binding	Interacting selectively and non-covalently with ubiquinone, a quinone derivative with a tail of isoprene units.
biological process
	GO:0044205	'de novo' UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	GO:0007565	female pregnancy	The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
	GO:0007595	lactation	The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
	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:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0090140	regulation of mitochondrial fission	Any process that modulates the rate, frequency or extent of mitochondrial fission. Mitochondrial fission is the division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
	GO:1903576	response to L-arginine	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 L-arginine stimulus.
	GO:0031000	response to caffeine	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 caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0014070	response to organic cyclic compound	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 an organic cyclic compound stimulus.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	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.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric Unit
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	PYRD_RAT \| Q63707	:	1uuo 4ori

1uuo	RAT DIHYDROOROTATE DEHYDROGENASE (DHOD)IN COMPLEX WITH BREQUINAR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (27, 27)

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Related Entries Specified in the PDB File