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(-) Description

Title :  X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH 2P-AMP AT 2.37 ANGSTROMS RESOLUTION
 
Authors :  I. Perez-Dorado, J. A. Hermoso
Date :  05 Feb 08  (Deposition) - 11 Nov 08  (Release) - 20 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A
Keywords :  Electron Transfer, Rhodobacter Capsulatus, Ferredoxin(Flavodoxin)-Nadp(H) Reductase, Nadp, Flavoproteins, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bortolotti, I. Perez-Dorado, G. Goni, M. Medina, J. A. Hermoso, N. Carrillo, N. Cortez
Coenzyme Binding And Hydride Transfer In Rhodobacter Capsulatus Ferredoxin/Flavodoxin Nadp(H) Oxidoreductase.
Biochim. Biophys. Acta V. 1794 199 2009
PubMed-ID: 18973834  |  Reference-DOI: 10.1016/J.BBAPAP.2008.09.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NADPH:FERREDOXIN REDUCTASE
    Chains: A
    EC Number: 1.18.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: RHODOBACTER CAPSULATUS
    Organism Taxid: 1061
    Strain: 37B4
    Synonym: FERREDOXIN-NADP REDUCTASE
    Variant: DSM938

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1A2P1Ligand/IonADENOSINE-2'-5'-DIPHOSPHATE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3HTG1Ligand/IonHEPTYL 1-THIOHEXOPYRANOSIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:49 , ARG A:64 , ALA A:65 , TYR A:66 , SER A:67 , TYR A:80 , SER A:81 , ILE A:82 , VAL A:84 , GLY A:87 , PRO A:88 , LEU A:89 , THR A:90 , THR A:130 , ALA A:133 , LYS A:265 , ALA A:266 , PHE A:267 , VAL A:268 , GLY A:271 , ILE A:272 , HOH A:2033 , HOH A:2070 , HOH A:2071BINDING SITE FOR RESIDUE FAD A 273
2AC2SOFTWARETHR A:128 , ALA A:156 , CYS A:157 , ARG A:158 , THR A:194 , ARG A:195 , ARG A:203 , THR A:205 , ALA A:236 , PHE A:237 , ASP A:240 , HOH A:2050 , HOH A:2057 , HOH A:2073BINDING SITE FOR RESIDUE A2P A 274
3AC3SOFTWARELEU A:54 , LEU A:55 , GLU A:100 , GLN A:101 , ILE A:103BINDING SITE FOR RESIDUE HTG A 275

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VNI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VNI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VNI)

(-) Exons   (0, 0)

(no "Exon" information available for 2VNI)

(-) 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:257
 aligned with Q9L6V3_RHOCA | Q9L6V3 from UniProtKB/TrEMBL  Length:272

    Alignment length:257
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       
         Q9L6V3_RHOCA    16 PDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI 272
               SCOP domains d2vnia1 A:16-113 automated matches                                                                d2vnia2 A:114-272 automated matches                                                                                                                             SCOP domains
               CATH domains ----2vniA01 A:20-106 Translation factors                                                   ------2vniA02 A:113-266 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                     ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeee...........eeeeeee.....eeeeeee........eeeeeee......hhhhhh......eeeeeeeee...hhhh.....eeeeeee...hhhhhhhh.hhhhhhhh.eeeeeeee..hhhhhhhhhhhhhhhhh..hhhhhh..eeeeeee.........hhhhhhhhhhhhhhh.........eeeeeeehhhhhhhhhhhhhh.............eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vni A  16 PDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI 272
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265
   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, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9L6V3_RHOCA | Q9L6V3)
molecular function
    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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 Related Entries

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

UniProtKB/TrEMBL
        Q9L6V3_RHOCA | Q9L6V3: 2bgi 2bgj 2vnh 2vnj 2vnk 4k1x

(-) Related Entries Specified in the PDB File

2bgi X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H ) REDUCTASE FROM RHODOBACTER CAPSULATUS COMPLEXED WITH THREE MOLECULES OF THE DETERGENT N-HEPTYL-BETA-D-THIOGLUCOSIDE AT 1.7 ANGSTROMS
2bgj X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H ) REDUCTASE FROM RHODOBACTER CAPSULATUS AT 2 .1 ANGSTROMS
2vnh X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H ) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH NADP. FORM II AT 2.27 ANGSTROMS RESOLUTION
2vnj X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H ) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH NADP. FORM I AT 2.13 ANGSTROMS RESOLUTION
2vnk X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H ) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH NADP. FORM III AT 1.93 ANGSTROMS RESOLUTION