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(-) Description

Title :  CRYSTAL STRUCTURE OF SIR-FP60
 
Authors :  A. Gruez, D. Pignol, M. Zeghouf, J. Coves, M. Fontecave, J. L. Ferrer, J. C. Fontecilla-Camps
Date :  10 Nov 99  (Deposition) - 13 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome P450 Reductase, Fnr, Flavoprotein, Modular Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gruez, D. Pignol, M. Zeghouf, J. Coves, M. Fontecave, J. L. Ferrer, J. C. Fontecilla-Camps
Four Crystal Structures Of The 60 Kda Flavoprotein Monomer Of The Sulfite Reductase Indicate A Disordered Flavodoxin-Like Module.
J. Mol. Biol. V. 299 199 2000
PubMed-ID: 10860732  |  Reference-DOI: 10.1006/JMBI.2000.3748
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SULFITE REDUCTASE [NADPH] FLAVOPROTEIN ALPHA- COMPONENT
    Chains: A
    EC Number: 1.8.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SIR-FP60
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:322 , VAL A:323 , ALA A:356 , ARG A:386 , LEU A:387 , TYR A:388 , SER A:389 , THR A:404 , VAL A:405 , GLY A:406 , TYR A:410 , GLY A:419 , GLY A:420 , ALA A:421 , SER A:422 , THR A:462 , ASP A:597 , TYR A:599 , HOH A:606 , HOH A:609 , HOH A:640 , HOH A:651 , HOH A:664 , HOH A:698 , HOH A:713 , HOH A:810 , HOH A:822 , HOH A:896BINDING SITE FOR RESIDUE FAD A 600
2AC2SOFTWARELYS A:254 , ASN A:489 , SER A:519 , ARG A:520 , LYS A:525 , TYR A:527 , GLN A:529 , MET A:558 , ASP A:561 , HOH A:621 , HOH A:781 , HOH A:786BINDING SITE FOR RESIDUE NAP A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DDI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.CYSJ_ECOLI234-448  1A:234-448

(-) Exons   (0, 0)

(no "Exon" information available for 1DDI)

(-) 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:374
 aligned with CYSJ_ECOLI | P38038 from UniProtKB/Swiss-Prot  Length:599

    Alignment length:374
                                   235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595    
           CYSJ_ECOLI   226 IHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEIDLGDSGMRYQPGDALGVWYQNDPALVKELVELLWLKGDEPVTVEGKTLPLNEALQWHFELTVNTANIVENYATLTRSETLLPLVGDKAKLQHYAATTPIVDMVRFSPAQLDAEALINLLRPLTPRLYSIASSQAEVENEVHVTVGVVRYDVEGRARAGGASSFLADRVEEEGEVRVFIEHNDNFRLPANPETPVIMIGPGTGIAPFRAFMQQRAADEAPGKNWLFFGNPHFTEDFLYQVEWQRYVKDGVLTRIDLAWSRDQKEKVYVQDKLREQGAELWRWINDGAHIYVCGDANRMAKDVEQALLEVIAEFGGMDTEAADEFLSELRVERRYQRDVY 599
               SCOP domains d1ddia1 A:226-446 Sulfite reductase flavoprotein                                                                                                                                                                             d1ddia2 A:447-599 Sulfite reductase flavoprotein                                                                                                          SCOP domains
               CATH domains 1ddiA01 A:226-279,A:385-444 Translation factors       1ddiA02 A:280-384 NADPH-cytochrome p450 Reductase; Chain A, domain 3                                     1ddiA01 A:226-279,A:385-444 Translation factors             1ddiA03 A:445-599 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeee.........eeeeeee............eeee....hhhhhhhhhhhh......eeee......hhhhhhhh......hhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhh..................eeee..........eeeeeee..eeee..eeeehhhhhhhhhh.....eeeeeee..............eeee.hhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhh.hhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhhhh..eeeeeee............................hhhhhhhh...eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------FAD_FR  PDB: A:234-448 UniProt: 234-448                                                                                                                                                                                ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ddi A 226 IHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEIDLGDSGLRYQPGDALGVWYQNDPALVKELVELLWLKGDEPVTVEGKTLPLNEALQWHFELTVNTANIVENYATLTRSETLLPLVGDKAKLQHYAATTPIVDMVRFSPAQLDAEALINLLRPLTPRLYSIASSQAEVENEVHVTVGVVRYDVEGRARAGGASSFLADRVEEEGEVRVFIEHNDNFRLPANPETPVIMIGPGTGIAPFRAFMQQRAADEAPGKNWLFFGNPHFTEDFLYQVEWQRYVKEGVLTRIDLAWSRDQKEKVYVQDKLREQGAELWRWINDGAHIYVCGDANRMAKDVEQALLEVIAEFGGMDTEAADEFLSELRVERRYQRDVY 599
                                   235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DDI)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYSJ_ECOLI | P38038)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042602    riboflavin reductase (NADPH) activity    Catalysis of the reaction: reduced riboflavin + NADP+ = riboflavin + NADPH + 2 H+.
    GO:0004783    sulfite reductase (NADPH) activity    Catalysis of the reaction: hydrogen sulfide + 3 NADP+ + 3 H2O = sulfite + 3 NADPH + 3 H+.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0019344    cysteine biosynthetic process    The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
    GO:0070814    hydrogen sulfide biosynthetic process    The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.
    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:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
cellular component
    GO:0009337    sulfite reductase complex (NADPH)    A multisubunit iron flavoprotein, which in yeast is composed of 2 alpha and 2 beta subunits. Catalyzes the reduction of sulfite to sulfide.

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 Related Entries

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UniProtKB/Swiss-Prot
        CYSJ_ECOLI | P38038: 1ddg 1ykg

(-) Related Entries Specified in the PDB File

1ddg SECOND CRYSTAL FORM