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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF TRYPANOSOMA CRUZI DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH TT2-3-063

Authors :   D. K. Inaoka, M. Iida, T. Tabuchi, N. Lee, S. Hashimoto, S. Matsuoka, T. K T. Shiba, K. Sakamoto, S. Suzuki, E. O. Balogun, T. Nara, T. Aoki, M. Ino T. Honma, A. Tanaka, S. Harada, K. Kita

Date :   02 Mar 13 (Deposition) - 05 Mar 14 (Release) - 05 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Rossmann Fold, Oxidoreductase, Dihydroorotate/Orotate And Fumarate/Succinate Binding, Cytosol, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. K. Inaoka, M. Iida, T. Tabuchi, N. Lee, S. Hashimoto, S. Matsuoka, T. Kuranaga, T. Shiba, K. Sakamoto, S. Suzuki, E. O. Balogun, T. Nara, T. Aoki, M. Inoue, T. Honma, A. Tanaka, S. Harada, K. Kita
Structure Of Trypanosoma Cruzi Dihydroorotate Dehydrogenase In Complex With Tt2-3-063
To Be Published
PubMed: search

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE (FUMARATE)
	Chains	:	A, B
	EC Number	:	1.3.98.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PYRD
	Organism Scientific	:	TRYPANOSOMA CRUZI
	Organism Taxid	:	353153
	Strain	:	CL BRENER
	Synonym	:	DHOD, DHODASE, DHODEHASE, DIHYDROOROTATE OXIDASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 22)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	GOL	17	Ligand/Ion	GLYCEROL
3	NCO	1	Ligand/Ion	COBALT HEXAMMINE(III)
4	W7M	2	Ligand/Ion	5-{2-[6-(METHOXYCARBONYL)NAPHTHALEN-2-YL]ETHYL}-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:43 , ASN A:53 , ASN A:67 , SER A:68 , MET A:69 , GLY A:70 , LEU A:71 , ASN A:127 , PRO A:131 , ASN A:194 , SER A:195 , LYS A:214 , FMN A:415 , HOH A:620	BINDING SITE FOR RESIDUE W7M A 401
02	AC2	SOFTWARE	CYS A:31 , ALA A:34 , SER A:35 , HOH A:530 , CYS B:31 , SER B:35 , PRO B:279 , HOH B:596	BINDING SITE FOR RESIDUE GOL A 402
03	AC3	SOFTWARE	PHE A:61 , VAL A:201 , ASP A:203	BINDING SITE FOR RESIDUE GOL A 403
04	AC4	SOFTWARE	TYR A:237 , ARG A:238 , PRO A:241	BINDING SITE FOR RESIDUE GOL A 404
05	AC5	SOFTWARE	LYS A:223 , TYR A:252 , ASP A:256 , HOH A:534 , HOH A:562 , LEU B:63	BINDING SITE FOR RESIDUE GOL A 405
06	AC6	SOFTWARE	TYR A:141 , PHE A:143 , HIS A:173 , GOL A:407 , HOH A:511 , HIS B:173	BINDING SITE FOR RESIDUE GOL A 406
07	AC7	SOFTWARE	HIS A:173 , GOL A:406 , HOH A:582 , TYR B:141 , HIS B:173	BINDING SITE FOR RESIDUE GOL A 407
08	AC8	SOFTWARE	VAL A:107 , ARG A:111 , GLN A:215 , ARG B:238 , GOL B:403	BINDING SITE FOR RESIDUE GOL A 408
09	AC9	SOFTWARE	VAL A:21 , LEU A:22 , ASP A:28 , GLN A:275 , GOL A:414	BINDING SITE FOR RESIDUE GOL A 409
10	BC1	SOFTWARE	LEU A:4 , ASN A:5 , GLU A:302 , ARG A:305 , ASN B:5 , VAL B:10	BINDING SITE FOR RESIDUE GOL A 410
11	BC2	SOFTWARE	PHE A:143 , GLU A:144 , ARG A:147 , THR A:176	BINDING SITE FOR RESIDUE GOL A 411
12	BC3	SOFTWARE	LYS A:223 , TYR A:252 , ARG A:284 , HOH A:595	BINDING SITE FOR RESIDUE GOL A 412
13	BC4	SOFTWARE	ASP A:203	BINDING SITE FOR RESIDUE GOL A 413
14	BC5	SOFTWARE	TYR A:58 , MET A:69 , GLN A:275 , GOL A:409	BINDING SITE FOR RESIDUE GOL A 414
15	BC6	SOFTWARE	ALA A:18 , ALA A:19 , GLY A:20 , LYS A:43 , SER A:44 , TYR A:58 , ASN A:67 , ASN A:127 , LYS A:164 , VAL A:193 , ASN A:194 , GLY A:221 , GLY A:222 , ILE A:225 , CYS A:248 , GLY A:249 , GLY A:250 , GLY A:271 , THR A:272 , W7M A:401 , HOH A:508 , HOH A:517 , HOH A:527	BINDING SITE FOR RESIDUE FMN A 415
16	BC7	SOFTWARE	GLN A:275 , GLU A:276 , GLY A:278 , GLN B:275 , GLU B:276 , GLY B:278	BINDING SITE FOR RESIDUE NCO A 416
17	BC8	SOFTWARE	LYS B:43 , ASN B:53 , ASN B:67 , MET B:69 , GLY B:70 , LEU B:71 , ASN B:127 , CYS B:130 , PRO B:131 , ASN B:194 , SER B:195 , LYS B:214 , FMN B:406	BINDING SITE FOR RESIDUE W7M B 401
18	BC9	SOFTWARE	ARG A:238 , ARG A:239 , LYS B:214 , PHE B:217	BINDING SITE FOR RESIDUE GOL B 402
19	CC1	SOFTWARE	ARG A:111 , LYS A:214 , PHE A:217 , GOL A:408 , ILE B:171 , ARG B:238 , ARG B:239	BINDING SITE FOR RESIDUE GOL B 403
20	CC2	SOFTWARE	TYR B:58 , MET B:69 , GLN B:275 , HOH B:563	BINDING SITE FOR RESIDUE GOL B 404
21	CC3	SOFTWARE	TYR B:237 , PRO B:241 , HOH B:535 , HOH B:599	BINDING SITE FOR RESIDUE GOL B 405
22	CC4	SOFTWARE	ALA B:18 , ALA B:19 , GLY B:20 , LYS B:43 , SER B:44 , ASN B:67 , ASN B:127 , LYS B:164 , VAL B:193 , ASN B:194 , GLY B:221 , GLY B:222 , CYS B:248 , GLY B:249 , GLY B:250 , GLY B:271 , THR B:272 , W7M B:401 , HOH B:505 , HOH B:521	BINDING SITE FOR RESIDUE FMN B 406

Asymmetric/Biological Unit

No.	Residues
1	A:1	-	B:1

Asymmetric/Biological Unit

No.	Residues
1	Glu A:55	-	Pro A:56
2	Cys A:192	-	Val A:193
3	Glu B:55	-	Pro B:56
4	Cys B:192	-	Val B:193

Asymmetric/Biological Unit (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PYRD_TRYCC_001 *	M	2	T	PYRD_TRYCC	---	---	A/B	M	0	T
2	UniProt	VAR_PYRD_TRYCC_002 *	C	3	R	PYRD_TRYCC	---	---	A/B	C	1	R
3	UniProt	VAR_PYRD_TRYCC_003 *	F	63	V	PYRD_TRYCC	---	---	A/B	F	61	V
4	UniProt	VAR_PYRD_TRYCC_004 *	S	86	I	PYRD_TRYCC	---	---	A/B	S	84	I
5	UniProt	VAR_PYRD_TRYCC_005 *	L	98	V	PYRD_TRYCC	---	---	A/B	L	96	V
6	UniProt	VAR_PYRD_TRYCC_006 *	L	222	I	PYRD_TRYCC	---	---	A/B	L	220	I
7	UniProt	VAR_PYRD_TRYCC_007 *	T	285	R	PYRD_TRYCC	---	---	A/B	T	283	R
8	UniProt	VAR_PYRD_TRYCC_008 *	R	301	K	PYRD_TRYCC	---	---	A/B	R	299	K
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3W7M)

(no "Exon" information available for 3W7M)

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:313
 aligned with PYRD_TRYCC | Q4D3W2 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311   
           PYRD_TRYCC     2 MCLKLNLLDHVFANPFMNAAGVLCSTEEDLRCMTASSSGALVSKSCTSAPRDGNPEPRYMAFPLGSINSMGLPNLGFDFYLKYASDLHDYSKKPLFLSISGLSVEENVAMVRRLAPVAQEKGVLLELNLSCPNVPGKPQVAYDFEAMRTYLQQVSLAYGLPFGVKMPPYFDIAHFDTAAAVLNEFPLVKFVTCVNSVGNGLVIDAESESVVIKPKQGFGGLGGKYILPTALANVNAFYRRCPDKLVFGCGGVYSGEDAFLHILAGASMVQVGTALQEEGPGIFTRLEDELLEIMARKGYRTLEEFRGRVKTIE 314
               SCOP domains d3w7ma_ A: Dihydroorotate dehydrogenase                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee...eee.......hhhhhhhhhhh....eeeeee............eeee..eeee.......hhhhhhhhhhh........eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.eeeeeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) TR-----------------------------------------------------------V----------------------I-----------V---------------------------------------------------------------------------------------------------------------------------I--------------------------------------------------------------R---------------K------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w7m A   0 MCLKLNLLDHVFANPFMNAAGVLCSTEEDLRCMTASSSGALVSKSCTSAPRDGNPEPRYMAFPLGSINSMGLPNLGFDFYLKYASDLHDYSKKPLFLSISGLSVEENVAMVRRLAPVAQEKGVLLELNLSCPNVPGKPQVAYDFEAMRTYLQQVSLAYGLPFGVKMPPYFDIAHFDTAAAVLNEFPLVKFVTCVNSVGNGLVIDAESESVVIKPKQGFGGLGGKYILPTALANVNAFYRRCPDKLVFGCGGVYSGEDAFLHILAGASMVQVGTALQEEGPGIFTRLEDELLEIMARKGYRTLEEFRGRVKTIE 312
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309

Chain B from PDB  Type:PROTEIN  Length:313
 aligned with PYRD_TRYCC | Q4D3W2 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311   
           PYRD_TRYCC     2 MCLKLNLLDHVFANPFMNAAGVLCSTEEDLRCMTASSSGALVSKSCTSAPRDGNPEPRYMAFPLGSINSMGLPNLGFDFYLKYASDLHDYSKKPLFLSISGLSVEENVAMVRRLAPVAQEKGVLLELNLSCPNVPGKPQVAYDFEAMRTYLQQVSLAYGLPFGVKMPPYFDIAHFDTAAAVLNEFPLVKFVTCVNSVGNGLVIDAESESVVIKPKQGFGGLGGKYILPTALANVNAFYRRCPDKLVFGCGGVYSGEDAFLHILAGASMVQVGTALQEEGPGIFTRLEDELLEIMARKGYRTLEEFRGRVKTIE 314
               SCOP domains d3w7mb_ B: Dihydroorotate dehydrogenase                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee...eee.......hhhhhhhhhhh....ee................eeee..eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhh....... Sec.struct. author
                 SAPs(SNPs) TR-----------------------------------------------------------V----------------------I-----------V---------------------------------------------------------------------------------------------------------------------------I--------------------------------------------------------------R---------------K------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w7m B   0 MCLKLNLLDHVFANPFMNAAGVLCSTEEDLRCMTASSSGALVSKSCTSAPRDGNPEPRYMAFPLGSINSMGLPNLGFDFYLKYASDLHDYSKKPLFLSISGLSVEENVAMVRRLAPVAQEKGVLLELNLSCPNVPGKPQVAYDFEAMRTYLQQVSLAYGLPFGVKMPPYFDIAHFDTAAAVLNEFPLVKFVTCVNSVGNGLVIDAESESVVIKPKQGFGGLGGKYILPTALANVNAFYRRCPDKLVFGCGGVYSGEDAFLHILAGASMVQVGTALQEEGPGIFTRLEDELLEIMARKGYRTLEEFRGRVKTIE 312
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309

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: Dihydroorotate dehydrogenase (90)

Trypanosoma cruzi [TaxId: 353153] (49)

1a	d3w7ma_	A:
1b	d3w7mb_	B:

(no "CATH Domain" information available for 3W7M)

(no "Pfam Domain" information available for 3W7M)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PYRD_TRYCC | Q4D3W2)

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:1990663	dihydroorotate dehydrogenase (fumarate) activity	Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate + succinate.
	GO:0004152	dihydroorotate dehydrogenase activity	Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate.
	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: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:0006222	UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate.
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Cys A:192 - Val A:193	[ RasMol ]
		Cys B:192 - Val B:193	[ RasMol ]
		Glu A:55 - Pro A:56	[ RasMol ]
		Glu B:55 - Pro B:56	[ RasMol ]

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	3w7m
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	PYRD_TRYCC \| Q4D3W2
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 22)

Sites (22, 22)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

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Exons (0, 0)

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