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(-) Description

Title :  STRUCTURE OF TRYPANOSOMA CRUZI DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH TT2-5-127
 
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 :  1.83
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 Tt2-5-127
To Be Published
PubMed: search

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 28)

Asymmetric/Biological Unit (4, 28)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2GOL23Ligand/IonGLYCEROL
3NCO1Ligand/IonCOBALT HEXAMMINE(III)
4W7Q2Ligand/Ion5-{2-[1-(TERT-BUTOXYCARBONYL)-2,3-DIHYDRO-1H-INDOL-5-YL]ETHYL}-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:43 , ARG A:50 , ASN A:53 , ASN A:67 , SER A:68 , MET A:69 , GLY A:70 , LEU A:71 , ASN A:127 , SER A:129 , PRO A:131 , ASN A:194 , SER A:195 , GOL A:411 , FMN A:413 , HOH A:851BINDING SITE FOR RESIDUE W7Q A 401
02AC2SOFTWARECYS A:31 , ALA A:34 , SER A:35 , PRO A:279 , HOH A:532 , CYS B:31 , ALA B:34 , SER B:35 , PRO B:279 , HOH B:656BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWAREILE A:171 , ARG A:239 , HOH A:596 , HOH A:758 , LYS B:214 , PHE B:217 , GOL B:408BINDING SITE FOR RESIDUE GOL A 403
04AC4SOFTWARELYS A:214 , PHE A:217 , HOH A:553 , ILE B:171 , ARG B:239BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWARETYR A:237 , PRO A:241 , GOL A:408 , HOH A:856BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWARELEU A:4 , ASN A:5 , GLU A:302 , ARG A:305 , HOH A:738 , HOH A:783 , HOH A:784 , HOH A:790 , LYS B:3 , ASN B:5 , VAL B:10BINDING SITE FOR RESIDUE GOL A 406
07AC7SOFTWARETYR A:58 , MET A:69 , GLN A:275 , HOH A:540BINDING SITE FOR RESIDUE GOL A 407
08AC8SOFTWARETYR A:237 , ARG A:238 , GOL A:405 , HOH A:587 , HOH A:669 , HOH B:681BINDING SITE FOR RESIDUE GOL A 408
09AC9SOFTWARETHR A:25 , GLU A:27 , ASP A:28 , HOH A:594 , HOH A:693 , GLU B:277 , ARG B:284BINDING SITE FOR RESIDUE GOL A 409
10BC1SOFTWAREPHE A:61 , ASP A:203 , HOH A:578 , HOH A:665 , HOH A:678BINDING SITE FOR RESIDUE GOL A 410
11BC2SOFTWARESER A:129 , CYS A:130 , PRO A:131 , GLN A:138 , ASN A:194 , SER A:195 , GLY A:197 , GLY A:219 , W7Q A:401 , HOH A:530 , HOH A:766 , HOH A:850 , HOH A:851BINDING SITE FOR RESIDUE GOL A 411
12BC3SOFTWAREASP A:203 , SER A:206 , SER A:208 , VAL A:209 , HOH A:576 , HOH A:678BINDING SITE FOR RESIDUE GOL A 412
13BC4SOFTWAREALA A:18 , ALA A:19 , GLY A:20 , LYS A:43 , SER A:44 , ASN A:67 , LYS A:164 , VAL A:193 , ASN A:194 , GLY A:222 , ILE A:225 , CYS A:248 , GLY A:249 , GLY A:250 , GLY A:271 , THR A:272 , W7Q A:401 , HOH A:509 , HOH A:517 , HOH A:528 , HOH A:759BINDING SITE FOR RESIDUE FMN A 413
14BC5SOFTWAREGLN A:275 , GLU A:276 , GLY A:278 , HOH A:730 , HOH A:810 , GLN B:275 , GLU B:276 , GLY B:278BINDING SITE FOR RESIDUE NCO A 414
15BC6SOFTWARELYS B:43 , ARG B:50 , ASN B:53 , ASN B:67 , SER B:68 , MET B:69 , GLY B:70 , LEU B:71 , ASN B:127 , SER B:129 , PRO B:131 , ASN B:194 , SER B:195 , GOL B:402 , FMN B:414BINDING SITE FOR RESIDUE W7Q B 401
16BC7SOFTWARESER B:129 , GLN B:138 , PRO B:166 , ASN B:194 , SER B:195 , GLY B:197 , W7Q B:401 , HOH B:514 , HOH B:519 , HOH B:744BINDING SITE FOR RESIDUE GOL B 402
17BC8SOFTWARETYR B:237 , ARG B:238 , PRO B:241 , GOL B:411 , HOH B:537 , HOH B:799BINDING SITE FOR RESIDUE GOL B 403
18BC9SOFTWARESER A:47 , HOH A:662 , ARG B:239 , HOH B:579 , HOH B:662 , HOH B:741BINDING SITE FOR RESIDUE GOL B 404
19CC1SOFTWAREHIS B:9 , TYR B:89 , LYS B:92 , PRO B:93 , LYS B:120 , GLY B:121 , GOL B:410 , HOH B:510 , HOH B:700BINDING SITE FOR RESIDUE GOL B 405
20CC2SOFTWAREPHE B:61 , VAL B:201 , ILE B:202 , ASP B:203 , HOH B:604 , HOH B:684 , HOH B:687BINDING SITE FOR RESIDUE GOL B 406
21CC3SOFTWAREILE A:311 , SER B:206 , SER B:208 , VAL B:209 , VAL B:210 , HOH B:623 , HOH B:684BINDING SITE FOR RESIDUE GOL B 407
22CC4SOFTWAREARG A:238 , GOL A:403 , GLN B:215 , HOH B:681 , HOH B:823BINDING SITE FOR RESIDUE GOL B 408
23CC5SOFTWARETYR B:58BINDING SITE FOR RESIDUE GOL B 409
24CC6SOFTWAREVAL B:10 , TYR B:89 , SER B:90 , LYS B:91 , PRO B:93 , GOL B:405 , HOH B:512 , HOH B:732 , HOH B:757BINDING SITE FOR RESIDUE GOL B 410
25CC7SOFTWAREPRO B:241 , LYS B:243 , GOL B:403 , HOH B:660BINDING SITE FOR RESIDUE GOL B 411
26CC8SOFTWAREGLN A:215 , ARG B:238 , GLY B:306 , VAL B:308 , THR B:310 , HOH B:533 , HOH B:552BINDING SITE FOR RESIDUE GOL B 412
27CC9SOFTWAREPRO B:49 , ARG B:50 , ASP B:51 , HOH B:556 , HOH B:819BINDING SITE FOR RESIDUE GOL B 413
28DC1SOFTWAREALA 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 , W7Q B:401 , HOH B:505 , HOH B:517 , HOH B:522 , HOH B:742BINDING SITE FOR RESIDUE FMN B 414

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1 -B:1

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Glu A:55 -Pro A:56
2Cys A:192 -Val A:193
3Met B:0 -Cys B:1
4Glu B:55 -Pro B:56
5Cys B:192 -Val B:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 16)

Asymmetric/Biological Unit (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PYRD_TRYCC_001 *M2TPYRD_TRYCC  ---  ---A/BM0T
2UniProtVAR_PYRD_TRYCC_002 *C3RPYRD_TRYCC  ---  ---A/BC1R
3UniProtVAR_PYRD_TRYCC_003 *F63VPYRD_TRYCC  ---  ---A/BF61V
4UniProtVAR_PYRD_TRYCC_004 *S86IPYRD_TRYCC  ---  ---A/BS84I
5UniProtVAR_PYRD_TRYCC_005 *L98VPYRD_TRYCC  ---  ---A/BL96V
6UniProtVAR_PYRD_TRYCC_006 *L222IPYRD_TRYCC  ---  ---A/BL220I
7UniProtVAR_PYRD_TRYCC_007 *T285RPYRD_TRYCC  ---  ---A/BT283R
8UniProtVAR_PYRD_TRYCC_008 *R301KPYRD_TRYCC  ---  ---A/BR299K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W7Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3W7Q)

(-) Sequences/Alignments

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 d3w7qa_ A: 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....hhhhhhhhhhhh...eeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) TR-----------------------------------------------------------V----------------------I-----------V---------------------------------------------------------------------------------------------------------------------------I--------------------------------------------------------------R---------------K------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w7q 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 d3w7qb_ 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............... Sec.struct. author
                 SAPs(SNPs) TR-----------------------------------------------------------V----------------------I-----------V---------------------------------------------------------------------------------------------------------------------------I--------------------------------------------------------------R---------------K------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w7q 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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W7Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W7Q)

(-) Gene Ontology  (10, 10)

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.

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  3w7q
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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PYRD_TRYCC | Q4D3W2: 2djl 2djx 2e68 2e6a 2e6d 2e6f 3c3n 3w1a 3w1l 3w1m 3w1n 3w1p 3w1q 3w1r 3w1t 3w1u 3w1x 3w22 3w23 3w2j 3w2k 3w2l 3w2m 3w2n 3w2u 3w3o 3w6y 3w70 3w71 3w72 3w73 3w74 3w75 3w76 3w7c 3w7d 3w7e 3w7g 3w7h 3w7i 3w7j 3w7k 3w7l 3w7m 3w7n 3w7o 3w7p 3w83 3w84 3w85 3w86 3w87 3w88 4jd4 4jdb 5e93 5ea9

(-) Related Entries Specified in the PDB File

3w1a 3w1l 3w1m 3w1n 3w1p 3w1q 3w1r 3w1t 3w1u 3w1x 3w22 3w23 3w2j 3w2k 3w2l 3w2m 3w2n 3w2u 3w6y 3w70 3w71 3w72 3w73 3w74 3w75 3w76 3w7c 3w7d 3w7e 3w7g 3w7h 3w7i 3w7j 3w7k 3w7l 3w7m 3w7n 3w7o 3w7p 4jd4 4jdb