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Title :   DIDYDROOROTATE DEHYDROGENASE FROM LEISHMANIA MAJOR

Authors :   A. T. Cordeiro, P. R. Feliciano, M. C. Nonato

Date :   03 Apr 09 (Deposition) - 07 Apr 10 (Release) - 07 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Alpha-Beta-Barrels, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. T. Cordeiro, P. R. Feliciano, M. C. Nonato
Crystal Structure Of Leishmania Major Dihydroorotate Dehydrogenase
To Be Published
PubMed: search

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE, PUTATIVE
	Chains	:	A, B
	EC Number	:	1.3.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LMJF16.0530, PYRD
	Organism Scientific	:	LEISHMANIA MAJOR
	Organism Taxid	:	5664
	Strain	:	FRIEDLIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:19 , ALA A:20 , GLY A:21 , LYS A:44 , SER A:45 , ASN A:68 , ASN A:128 , LYS A:165 , ILE A:194 , ASN A:195 , GLY A:222 , GLY A:223 , VAL A:226 , CYS A:249 , GLY A:250 , GLY A:251 , GLY A:272 , THR A:273 , HOH A:351 , HOH A:359 , HOH A:375	BINDING SITE FOR RESIDUE FMN A 321
2	AC2	SOFTWARE	ILE A:203 , HOH A:428 , HOH A:508 , LEU B:231	BINDING SITE FOR RESIDUE GOL A 322
3	AC3	SOFTWARE	ALA B:19 , ALA B:20 , GLY B:21 , LYS B:44 , SER B:45 , ASN B:68 , ASN B:128 , LYS B:165 , ILE B:194 , ASN B:195 , GLY B:223 , CYS B:249 , GLY B:250 , GLY B:251 , GLY B:272 , THR B:273 , HOH B:337 , HOH B:338 , HOH B:340	BINDING SITE FOR RESIDUE FMN B 321
4	AC4	SOFTWARE	LEU A:231 , HOH A:455 , VAL B:202 , ILE B:203 , HOH B:483	BINDING SITE FOR RESIDUE GOL B 322

(no "SS Bond" information available for 3GYE)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:56	-	Pro A:57
2	Cys A:193	-	Ile A:194
3	Thr B:56	-	Pro B:57
4	Cys B:193	-	Ile B:194

(no "SAP(SNP)/Variant" information available for 3GYE)

(no "PROSITE Motif" information available for 3GYE)

(no "Exon" information available for 3GYE)

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:299
 aligned with Q4QEW7_LEIMA | Q4QEW7 from UniProtKB/TrEMBL  Length:320

    Alignment length:312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
         Q4QEW7_LEIMA     1 MSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLSCPNVPGKPQVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
               SCOP domains d3gyea_ A: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3gyeA01 A:1-53,A:72-196,A:223-312 Aldolase class I   3gyeA02           3gyeA01 A:1-53,A:72-196,A:223-312 Aldolase class I                                                                           3gyeA02 A:54-71,A:197-222 3gyeA01 A:1-53,A:72-196,A:223-312 Aldolase class I                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..eee...eee.......hhhhhhhhhhh....eeeeee............eeee..eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee.-------------hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh...eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gye A   1 MSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNL-------------DFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
                                    10        20        30        40        50        60        70        80        90       100       110       120        |-         -  |    150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
                                                                                                                                                          129           143

Chain B from PDB  Type:PROTEIN  Length:299
 aligned with Q4QEW7_LEIMA | Q4QEW7 from UniProtKB/TrEMBL  Length:320

    Alignment length:312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
         Q4QEW7_LEIMA     1 MSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLSCPNVPGKPQVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
               SCOP domains d3gyeb_ B: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3gyeB01 B:1-53,B:72-196,B:223-312 Aldolase class I   3gyeB02           3gyeB01 B:1-53,B:72-196,B:223-312 Aldolase class I                                                                           3gyeB02 B:54-71,B:197-222 3gyeB01 B:1-53,B:72-196,B:223-312 Aldolase class I                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..eee...eee.......hhhhhhhhhhh....eeeeee............eeee..eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee.-------------hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh...eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gye B   1 MSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNL-------------DFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
                                    10        20        30        40        50        60        70        80        90       100       110       120        |-         -  |    150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
                                                                                                                                                          129           143

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) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: FMN-linked oxidoreductases (290)

Family: FMN-linked oxidoreductases (242)

Protein domain: automated matches (40)

Leishmania major [TaxId: 5664] (6)

1a	d3gyea_	A:
1b	d3gyeb_	B:

Asymmetric/Biological 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)

Leishmania major. Organism_taxid: 5664. Strain: friedlin. (2)

1a	3gyeA01	A:1-53,A:72-196,A:223-312
1b	3gyeB01	B:1-53,B:72-196,B:223-312

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Dihydroorotate Dehydrogenase A; chain A, domain 2 (22)

Homologous Superfamily: Dihydroorotate Dehydrogenase A, chain A, domain 2 (22)

Leishmania major. Organism_taxid: 5664. Strain: friedlin. (2)

2a	3gyeA02	A:54-71,A:197-222
2b	3gyeB02	B:54-71,B:197-222

(no "Pfam Domain" information available for 3GYE)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q4QEW7_LEIMA | Q4QEW7)

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:0004152	dihydroorotate dehydrogenase activity	Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate.
	GO:0004158	dihydroorotate oxidase activity	Catalysis of the reaction: (S)-dihydroorotate + O(2) = H(2)O(2) + orotate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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: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:0006222	UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate.
	GO:0006106	fumarate metabolic process	The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0020015	glycosome	A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Cys A:193 - Ile A:194	[ RasMol ]
		Cys B:193 - Ile B:194	[ RasMol ]
		Thr A:56 - Pro A:57	[ RasMol ]
		Thr B:56 - Pro B:57	[ RasMol ]

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	Q4QEW7_LEIMA \| Q4QEW7	:	3gz3 3mhu 3mjy 3tjx 3tq0 3tro 4ef8 4ef9

3c3n	TRYPANOSOMA CRUZI DHODH
3gz3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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