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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE FERREDOXIN-NADP+ REDUCTASE FROM PAPRIKA
 
Authors :  A. Dorowski, A. Hofmann, C. Steegborn, M. Boicu, R. Huber
Date :  08 Mar 04  (Deposition) - 16 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Rossmann Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dorowski, A. Hofmann, C. Steegborn, M. Boicu, R. Huber
Crystal Structure Of Paprika Ferredoxin-Nadp+ Reductase. Implications For The Electron Transfer Pathway.
J. Biol. Chem. V. 276 9253 2001
PubMed-ID: 11053431  |  Reference-DOI: 10.1074/JBC.M004576200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHLOROPLAST FERREDOXIN-NADP+ OXIDOREDUCTASE
    Chains: A, B
    EC Number: 1.18.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: CAPSICUM ANNUUM
    Organism Taxid: 4072

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:282 , ARG A:283 , LYS A:292 , TYR A:294BINDING SITE FOR RESIDUE PO4 A 363
2AC2SOFTWAREGLY B:1074 , SER B:1282 , ARG B:1283 , LYS B:1292 , TYR B:1294BINDING SITE FOR RESIDUE PO4 B 1363
3AC3SOFTWAREARG A:141 , LEU A:142 , TYR A:143 , SER A:144 , CYS A:162 , VAL A:163 , LYS A:164 , LEU A:166 , TYR A:168 , ASN A:170 , GLY A:178 , VAL A:179 , CYS A:180 , SER A:181 , THR A:220 , GLU A:360 , TYR A:362 , HOH A:374 , HOH A:432 , HOH A:506 , HOH A:513 , HOH A:566BINDING SITE FOR RESIDUE FAD A 364
4AC4SOFTWARESER B:1123 , ARG B:1141 , LEU B:1142 , TYR B:1143 , SER B:1144 , CYS B:1162 , VAL B:1163 , LYS B:1164 , TYR B:1168 , ASN B:1170 , GLY B:1178 , VAL B:1179 , CYS B:1180 , SER B:1181 , THR B:1220 , GLU B:1360 , TYR B:1362 , HOH B:1378 , HOH B:1380 , HOH B:1381 , HOH B:1430 , HOH B:1442BINDING SITE FOR RESIDUE FAD B 1364

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SM4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:197 -Pro A:198
2Gly B:1197 -Pro B:1198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SM4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SM4)

(-) Exons   (0, 0)

(no "Exon" information available for 1SM4)

(-) Sequences/Alignments

Asymmetric 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:296
 aligned with Q9M4D2_CAPAN | Q9M4D2 from UniProtKB/TrEMBL  Length:362

    Alignment length:296
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      
        Q9M4D2_CAPAN     67 ISKKQDEGVVVNKFRPKEPYIGRCLLNTKITGDDAPGETWHMVFSTEGEIPYREGQSIGVIADGVDANGKPHKLRLYSIASSALGDFGDSKTVSLCVKRLVYTNDKGEEVKGVCSNFLCDLKPGADVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHDDYKFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQTNEKGEKMYIQTRMAQYAEELWTLLKKDNTFVYMCGLKGMEQGIDDIMSSLAAKEGIDWADYKKQLKKAEQWNVEVY  362
               SCOP domains d1sm4a1 A:67-207 Ferredoxin reductase (flavodoxin reductase) N-terminal domain                                                               d1sm4a2 A:208-362 Ferredoxin reductase (flavodoxin reductase)                                                                                               SCOP domains
               CATH domains 1sm4A01 A:67-199 Translation factors                                                                                                 1sm4A02 A:200-362 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeeeeee.........eeeeeee...........eeeee.............eeee.............eeeeeee..ee.......eehhhhhhhhh.....eeeeeeee............eeeeeee...hhhhhhhhhhhhh..........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1sm4 A   67 ISKKQDEGVVVNKFRPKEPYIGRCLLNTKITGDDAPGETWHMVFSTEGEIPYREGQSIGVIADGVDANGKPHKLRLYSIASSALGDFGDSKTVSLCVKRLVYTNDKGEEVKGVCSNFLCDLKPGADVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHDDYKFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQTNEKGEKMYIQTRMAQYAEELWTLLKKDNTFVYMCGLKGMEQGIDDIMSSLAAKEGIDWADYKKQLKKAEQWNVEVY  362
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      


Chain B from PDB  Type:PROTEIN  Length:296
 aligned with Q9M4D2_CAPAN | Q9M4D2 from UniProtKB/TrEMBL  Length:362

    Alignment length:296
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      
        Q9M4D2_CAPAN     67 ISKKQDEGVVVNKFRPKEPYIGRCLLNTKITGDDAPGETWHMVFSTEGEIPYREGQSIGVIADGVDANGKPHKLRLYSIASSALGDFGDSKTVSLCVKRLVYTNDKGEEVKGVCSNFLCDLKPGADVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHDDYKFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQTNEKGEKMYIQTRMAQYAEELWTLLKKDNTFVYMCGLKGMEQGIDDIMSSLAAKEGIDWADYKKQLKKAEQWNVEVY  362
               SCOP domains d1sm4b1 B:1067-1207 Ferredoxin reductase (flavodoxin reductase) N-terminal domain                                                            d1sm4b2 B:1208-1362 Ferredoxin reductase (flavodoxin reductase)                                                                                             SCOP domains
               CATH domains 1sm4B01 B:1067-1199 Translation factors                                                                                              1sm4B02 B:1200-1362 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                             CATH domains
           Pfam domains (1) ----------------------------------------FAD_binding_6-1sm4B01 B:1107-1204                                                                 ----------NAD_binding_1-1sm4B03 B:1215-1331                                                                                    ------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------FAD_binding_6-1sm4B02 B:1107-1204                                                                 ----------NAD_binding_1-1sm4B04 B:1215-1331                                                                                    ------------------------------- Pfam domains (2)
         Sec.struct. author ...................eeeeeeeeee.........eeeeeee...........eeeee.............eeee.............eeeeeee..ee.......eehhhhhhhhh.....eeeeeeee............eeeeeee..hhhhhhhhhhhhhh..........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhh.hhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1sm4 B 1067 ISKKQDEGVVVNKFRPKEPYIGRCLLNTKITGDDAPGETWHMVFSTEGEIPYREGQSIGVIADGVDANGKPHKLRLYSIASSALGDFGDSKTVSLCVKRLVYTNDKGEEVKGVCSNFLCDLKPGADVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHDDYKFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQTNEKGEKMYIQTRMAQYAEELWTLLKKDNTFVYMCGLKGMEQGIDDIMSSLAAKEGIDWADYKKQLKKAEQWNVEVY 1362
                                  1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316      1326      1336      1346      1356
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: FAD_Lum_binding (30)
(-)
Clan: NAD_Ferredoxin (30)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9M4D2_CAPAN | Q9M4D2)
molecular function
    GO:0004324    ferredoxin-NADP+ reductase activity    Catalysis of the reaction: reduced ferredoxin + NADP+ = oxidized ferredoxin + NADPH + H+.
    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.
biological process
    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.

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