2DJX - JenaLib

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Title :   CRYSTAL STRUCTURE OF NATIVE TRYPANOSOMA CRUZI DIHYDROOROTATE DEHYDROGENASE

Authors :   D. K. Inaoka, H. Shimizu, K. Sakamoto, T. Shiba, G. Kurisu, T. Nara, T. Aoki, S. Harada, K. Kita

Date :   05 Apr 06 (Deposition) - 26 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.58

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

Keywords :   Chagas' Disease, Pyrimidine Biosynthesis, Fumarate Reductase, Energy Metabolism, Redox Homeostasis, Flavoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. K. Inaoka, H. Shimizu, K. Sakamoto, T. Shiba, G. Kurisu, T. Nara, T. Aoki, S. Harada, K. Kita
Crystal Structure Of Native Trypanosoma Cruzi Dihydroorotate Dehydrogenase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.3.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	TCDHOD2
	Organism Scientific	:	TRYPANOSOMA CRUZI
	Organism Taxid	:	5693
	Strain	:	TULAHUEN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	NCO	1	Ligand/Ion	COBALT HEXAMMINE(III)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:275 , GLU A:276 , HOH A:1534 , GLN B:275 , GLU B:276	BINDING SITE FOR RESIDUE NCO A 1351
2	AC2	SOFTWARE	ALA A:18 , ALA A:19 , GLY A:20 , LYS A:43 , SER A:44 , ASN A:67 , ASN A:127 , LYS A:164 , VAL A:193 , ASN A:194 , SER A:195 , GLY A:222 , ILE A:225 , CYS A:248 , GLY A:249 , GLY A:250 , GLY A:271 , THR A:272 , HOH A:1474 , HOH A:1488 , HOH A:1494 , HOH A:1543	BINDING SITE FOR RESIDUE FMN A 1350
3	AC3	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:222 , ILE B:225 , CYS B:248 , GLY B:249 , GLY B:250 , GLY B:271 , THR B:272 , HOH B:2487 , HOH B:2491 , HOH B:2506 , HOH B:2533	BINDING SITE FOR RESIDUE FMN B 2350

(no "SS Bond" information available for 2DJX)

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 2DJX)

(no "Exon" information available for 2DJX)

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 d2djxa_ A: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2djxA01 A:0-52,A:71-195,A:222-312 Aldolase class I   2djxA02           2djxA01 A:0-52,A:71-195,A:222-312 Aldolase class I                                                                           2djxA02 A:53-70,A:196-221 2djxA01 A:0-52,A:71-195,A:222-312 Aldolase class I                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee...eee........hhhhhhhhh.....eee...............eeee..eeee........hhhhhhhhhh........eeeee....hhhhhhhhhhhhhhhhhh..eeeee...........hhh...................eeee......hhhhhhhhhhhhh.....eeee.........eee..eee.........eee.hhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhh....eeehhhhhhh.hhhhhhhhhhhhhhhhhh....hhhh...eee.. Sec.struct. author
                 SAPs(SNPs) TR-----------------------------------------------------------V----------------------I-----------V---------------------------------------------------------------------------------------------------------------------------I--------------------------------------------------------------R---------------K------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2djx A   0 MCLKLNLLDHVFANPFMNAAGVLCCTEEDLRCMTASSSGALVSKSCTSAPRDGNPEPRYMAFPLGSINSMGLPNLGFDFYLKYASDLHDYSKKPLFLSISGLSVEENVAMVRRLAPVAQEKGVLLELNLSCPNVPGKPQVAYDFEAMRTYLQQVSLAYGLPFGVKMPPYFDIAHFDTAAAVLNEFPLVKFVTCVNSVGNGLVIDAESESVVIKPKQGFGGLGGKYILPTALANVNAFYRRCPDKLVFGCGGVYSGEDAFLHILAGASMVQVGTALQEEGPGIFTRLEDELLEIMARKGYRTLEEFRGRVKTIE 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 d2djxb_ B: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2djxB01 B:0-52,B:71-195,B:222-312 Aldolase class I   2djxB02           2djxB01 B:0-52,B:71-195,B:222-312 Aldolase class I                                                                           2djxB02 B:53-70,B:196-221 2djxB01 B:0-52,B:71-195,B:222-312 Aldolase class I                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee...eee........hhhhhhhhh.....eee...............eeee..eeee........hhhhhhhhhh........eeeee....hhhhhhhhhhhhhhhhhh..eeeee...........hhh...................eeee......hhhhhhhhhhhhh.....eeee.........eee..eee.........eee.hhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhh....eeehhhhhhh.hhhhhhhhhhhhhhhhhh....hhhh...eee.. Sec.struct. author
                 SAPs(SNPs) TR-----------------------------------------------------------V----------------------I-----------V---------------------------------------------------------------------------------------------------------------------------I--------------------------------------------------------------R---------------K------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2djx B   0 MCLKLNLLDHVFANPFMNAAGVLCCTEEDLRCMTASSSGALVSKSCTSAPRDGNPEPRYMAFPLGSINSMGLPNLGFDFYLKYASDLHDYSKKPLFLSISGLSVEENVAMVRRLAPVAQEKGVLLELNLSCPNVPGKPQVAYDFEAMRTYLQQVSLAYGLPFGVKMPPYFDIAHFDTAAAVLNEFPLVKFVTCVNSVGNGLVIDAESESVVIKPKQGFGGLGGKYILPTALANVNAFYRRCPDKLVFGCGGVYSGEDAFLHILAGASMVQVGTALQEEGPGIFTRLEDELLEIMARKGYRTLEEFRGRVKTIE 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: automated matches (40)

Trypanosoma cruzi [TaxId: 5693] (7)

1a	d2djxa_	A:
1b	d2djxb_	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)

Trypanosoma cruzi. Organism_taxid: 5693. Strain: tulahuen. (2)

1a	2djxA01	A:0-52,A:71-195,A:222-312
1b	2djxB01	B:0-52,B:71-195,B:222-312

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)

Trypanosoma cruzi. Organism_taxid: 5693. Strain: tulahuen. (2)

2a	2djxA02	A:53-70,A:196-221
2b	2djxB02	B:53-70,B:196-221

(no "Pfam Domain" information available for 2DJX)

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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	2djx
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2djl	THE SAME PROTEIN IN COMPLEX WITH SUCCINATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (10, 10)

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