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(-) Description

Title :  STRUCTURE OF TRYPANOSOMA CRUZI DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH MII-4-065
 
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 :  23 Feb 13  (Deposition) - 26 Feb 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
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 Mii-4-065
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, 23)

Asymmetric/Biological Unit (4, 23)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2GOL18Ligand/IonGLYCEROL
3JDM2Ligand/Ion5-{2-[2-(HYDROXYMETHYL)PHENYL]ETHYL}-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
4NCO1Ligand/IonCOBALT HEXAMMINE(III)

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:43 , ASN A:67 , MET A:69 , GLY A:70 , LEU A:71 , SER A:99 , LEU A:101 , ASN A:127 , SER A:129 , PRO A:131 , ASN A:194 , SER A:195 , GOL A:406 , FMN A:410 , HOH A:828BINDING SITE FOR RESIDUE JDM A 401
02AC2SOFTWAREGLN A:215 , HOH A:564 , HOH A:654 , HOH A:795 , ARG B:238 , GOL B:409BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWAREVAL A:10 , TYR A:89 , SER A:90 , PRO A:93 , GOL A:408 , HOH A:512 , HOH A:789BINDING SITE FOR RESIDUE GOL A 403
04AC4SOFTWAREMET A:69 , GLN A:275 , HOH A:574 , HOH A:648 , HOH A:687BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWAREILE A:171 , ARG A:239 , HOH A:554 , HOH A:820 , LYS B:214 , PHE B:217 , GOL B:405BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWARESER A:129 , GLN A:138 , PRO A:166 , ASN A:194 , SER A:195 , GLY A:197 , JDM A:401 , HOH A:513 , HOH A:518 , HOH A:828BINDING SITE FOR RESIDUE GOL A 406
07AC7SOFTWARETYR A:237 , PRO A:241 , HOH A:536 , HOH A:819BINDING SITE FOR RESIDUE GOL A 407
08AC8SOFTWAREHIS A:9 , TYR A:89 , LYS A:92 , PRO A:93 , LYS A:120 , GLY A:121 , GOL A:403 , HOH A:510 , HOH A:716BINDING SITE FOR RESIDUE GOL A 408
09AC9SOFTWARETYR A:141 , PHE A:143 , HIS A:173 , HOH A:611 , HOH A:717 , HOH A:829 , HIS B:173 , GOL B:411BINDING SITE FOR RESIDUE GOL A 409
10BC1SOFTWAREALA 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 , GLY A:221 , GLY A:222 , ILE A:225 , CYS A:248 , GLY A:249 , GLY A:250 , GLY A:271 , THR A:272 , JDM A:401 , HOH A:505 , HOH A:516 , HOH A:521 , HOH A:766BINDING SITE FOR RESIDUE FMN A 410
11BC2SOFTWARELYS B:43 , ASN B:67 , MET B:69 , GLY B:70 , LEU B:71 , SER B:99 , LEU B:101 , ASN B:127 , PRO B:131 , ASN B:194 , SER B:195 , GOL B:406 , FMN B:412 , HOH B:774BINDING SITE FOR RESIDUE JDM B 401
12BC3SOFTWARETYR B:58 , MET B:69 , HOH B:539 , HOH B:599 , HOH B:618BINDING SITE FOR RESIDUE GOL B 402
13BC4SOFTWAREASN A:5 , VAL A:10 , LEU B:4 , ASN B:5 , GLU B:302 , HOH B:745 , HOH B:795 , HOH B:796 , HOH B:825BINDING SITE FOR RESIDUE GOL B 403
14BC5SOFTWAREPHE B:61 , ASP B:203 , HOH B:574 , HOH B:658 , HOH B:674BINDING SITE FOR RESIDUE GOL B 404
15BC6SOFTWAREARG A:238 , GOL A:405 , HOH A:804 , GLU B:104 , VAL B:107 , ARG B:111 , GLN B:215 , HOH B:568 , HOH B:736BINDING SITE FOR RESIDUE GOL B 405
16BC7SOFTWARESER B:129 , GLN B:138 , PRO B:166 , ASN B:194 , SER B:195 , GLY B:197 , JDM B:401 , HOH B:521 , HOH B:529 , HOH B:774BINDING SITE FOR RESIDUE GOL B 406
17BC8SOFTWAREARG A:112 , HOH A:788 , ASP B:175 , THR B:176 , ALA B:179 , HOH B:789BINDING SITE FOR RESIDUE GOL B 407
18BC9SOFTWARECYS A:31 , ALA A:34 , SER A:35 , PRO A:279 , HOH A:665 , CYS B:31 , ALA B:34 , HOH B:531BINDING SITE FOR RESIDUE GOL B 408
19CC1SOFTWARELYS A:214 , PHE A:217 , GOL A:402 , ILE B:171 , ARG B:239 , HOH B:592 , HOH B:765BINDING SITE FOR RESIDUE GOL B 409
20CC2SOFTWARETYR B:237 , PRO B:241 , HOH B:567BINDING SITE FOR RESIDUE GOL B 410
21CC3SOFTWAREHIS A:173 , GOL A:409 , HOH A:829 , TYR B:141 , PHE B:143 , HIS B:173 , HOH B:581 , HOH B:847BINDING SITE FOR RESIDUE GOL B 411
22CC4SOFTWAREALA 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 , ILE B:225 , CYS B:248 , GLY B:249 , GLY B:250 , GLY B:271 , THR B:272 , JDM B:401 , HOH B:509 , HOH B:517 , HOH B:527 , HOH B:766BINDING SITE FOR RESIDUE FMN B 412
23CC5SOFTWAREGLN A:275 , GLU A:276 , GLY A:278 , GLN B:275 , GLU B:276 , GLY B:278 , HOH B:733BINDING SITE FOR RESIDUE NCO B 413

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JD4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JD4)

(-) Exons   (0, 0)

(no "Exon" information available for 4JD4)

(-) 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
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4jd4a_ 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....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jd4 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
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4jd4b_ B: Dihydroorotate dehydrogenase                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee...eee.......hhhhhhhhhhh....eeeeee............eeee..eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jd4 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 4JD4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JD4)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) 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 3w7q 3w83 3w84 3w85 3w86 3w87 3w88 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 4jdb