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(-) Description

Title :  OLD YELLOW ENZYME FROM THERMUS SCOTODUCTUS SA-01
 
Authors :  D. J. Opperman, B. T. Sewell, D. Litthauer, M. N. Isupov, J. A. Littlechi Heerden
Date :  11 May 09  (Deposition) - 23 Feb 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B  (2x)
Biol. Unit 3:  C  (2x)
Keywords :  Tim Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. J. Opperman, B. T. Sewell, D. Litthauer, M. N. Isupov, J. A. Littlechild, E. Van Heerden
Crystal Structure Of A Thermostable Old Yellow Enzyme From Thermus Scotoductus Sa-01
Biochem. Biophys. Res. Commun. V. 393 426 2010
PubMed-ID: 20138824  |  Reference-DOI: 10.1016/J.BBRC.2010.02.011

(-) Compounds

Molecule 1 - CHROMATE REDUCTASE
    ChainsA, B, C, D
    EC Number1.6.99.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCRS
    Organism ScientificTHERMUS SCOTODUCTUS
    Organism Taxid37636
    StrainSA-01

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (2x) B  
Biological Unit 3 (2x)  C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:22 , PRO A:23 , MET A:24 , CYS A:25 , ALA A:58 , GLN A:100 , HIS A:172 , HIS A:175 , ARG A:225 , VAL A:294 , GLY A:295 , LEU A:296 , GLY A:318 , ARG A:319 , HOH A:350 , HOH A:353 , HOH A:359 , HOH A:373 , HOH A:746 , SO4 A:1101 , ARG D:347BINDING SITE FOR RESIDUE FMN A 1001
2AC2SOFTWAREILE A:67 , HIS A:172 , HIS A:175 , TYR A:177 , HOH A:555 , HOH A:744 , FMN A:1001BINDING SITE FOR RESIDUE SO4 A 1101
3AC3SOFTWARESER B:22 , PRO B:23 , MET B:24 , CYS B:25 , ALA B:58 , GLN B:100 , HIS B:172 , HIS B:175 , ARG B:225 , VAL B:294 , LEU B:296 , GLY B:318 , ARG B:319 , ARG B:347 , HOH B:350 , HOH B:351 , HOH B:386 , HOH B:474 , SO4 B:1102BINDING SITE FOR RESIDUE FMN B 1002
4AC4SOFTWAREHIS B:172 , HIS B:175 , TYR B:177 , HOH B:514 , FMN B:1002BINDING SITE FOR RESIDUE SO4 B 1102
5AC5SOFTWARESER C:22 , PRO C:23 , MET C:24 , CYS C:25 , ALA C:58 , GLN C:100 , HIS C:172 , HIS C:175 , ARG C:225 , VAL C:294 , GLY C:295 , LEU C:296 , GLY C:318 , ARG C:319 , ARG C:347 , HOH C:351 , HOH C:352 , HOH C:392 , HOH C:412 , SO4 C:1103BINDING SITE FOR RESIDUE FMN C 1003
6AC6SOFTWAREHIS C:172 , HIS C:175 , TYR C:177 , HOH C:603 , FMN C:1003BINDING SITE FOR RESIDUE SO4 C 1103
7AC7SOFTWAREARG A:347 , SER D:22 , PRO D:23 , MET D:24 , CYS D:25 , ALA D:58 , GLN D:100 , HIS D:172 , HIS D:175 , ARG D:225 , VAL D:294 , GLY D:295 , LEU D:296 , GLY D:318 , ARG D:319 , HOH D:351 , HOH D:360 , HOH D:367 , HOH D:559 , SO4 D:1104BINDING SITE FOR RESIDUE FMN D 1004
8AC8SOFTWAREHIS D:172 , HIS D:175 , TYR D:177 , HOH D:772 , FMN D:1004BINDING SITE FOR RESIDUE SO4 D 1104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HF3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HF3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HF3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HF3)

(-) Exons   (0, 0)

(no "Exon" information available for 3HF3)

(-) 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:348
 aligned with B0JDW3_THESC | B0JDW3 from UniProtKB/TrEMBL  Length:349

    Alignment length:348
                                    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       321       331       341        
         B0JDW3_THESC     2 ALLFTPLELGGLRLKNRLAMSPMCQYSATLEGEVTDWHLLHYPTRALGGVGLILVEATAVEPLGRISPYDLGIWSEDHLPGLKELARRIREAGAVPGIQLAHAGRKAGTARPWEGGKPLGWRVVGPSPIPFDEGYPVPEPLDEAGMERILQAFVEGARRALRAGFQVIELHMAHGYLLSSFLSPLSNQRTDAYGGSLENRMRFPLQVAQAVREVVPRELPLFVRVSATDWGEGGWSLEDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPFADAVRKRVGLRTGAVGLITTPEQAETLLQAGSADLVLLGRVLLRDPYFPLRAAKALGVAPEVPPQYQRGF 349
               SCOP domains d3hf3a_ A: automated matches                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.eee..eee...eee..............hhhhhhhhhhhhhh...eeeeeeee.hhhhh.....ee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh...hhhhh........ee.............ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhh.......eeeeee.........hhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhh..eee.....hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhhh......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hf3 A   2 ALLFTPLELGGLRLKNRLAMSPMCQYSATLEGEVTDWHLLHYPTRALGGVGLILVEATAVEPLGRISPYDLGIWSEDHLPGLKELARRIREAGAVPGIQLAHAGRKAGTARPWEGGKPLGWRVVGPSPIPFDEGYPVPEPLDEAGMERILQAFVEGARRALRAGFQVIELHMAHGYLLSSFLSPLSNQRTDAYGGSLENRMRFPLQVAQAVREVVPRELPLFVRVSATDWGEGGWSLEDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPFADAVRKRVGLRTGAVGLITTPEQAETLLQAGSADLVLLGRVLLRDPYFPLRAAKALGVAPEVPPQYQRGF 349
                                    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       321       331       341        

Chain B from PDB  Type:PROTEIN  Length:348
 aligned with B0JDW3_THESC | B0JDW3 from UniProtKB/TrEMBL  Length:349

    Alignment length:348
                                    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       321       331       341        
         B0JDW3_THESC     2 ALLFTPLELGGLRLKNRLAMSPMCQYSATLEGEVTDWHLLHYPTRALGGVGLILVEATAVEPLGRISPYDLGIWSEDHLPGLKELARRIREAGAVPGIQLAHAGRKAGTARPWEGGKPLGWRVVGPSPIPFDEGYPVPEPLDEAGMERILQAFVEGARRALRAGFQVIELHMAHGYLLSSFLSPLSNQRTDAYGGSLENRMRFPLQVAQAVREVVPRELPLFVRVSATDWGEGGWSLEDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPFADAVRKRVGLRTGAVGLITTPEQAETLLQAGSADLVLLGRVLLRDPYFPLRAAKALGVAPEVPPQYQRGF 349
               SCOP domains d3hf3b_ B: automated matches                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.eee..eee...eee..............hhhhhhhhhhhhhh...eeeeeeee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh................ee.............ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhhh...eeeee................hhhhhhhhhhhhh.eeee.....hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhhh......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hf3 B   2 ALLFTPLELGGLRLKNRLAMSPMCQYSATLEGEVTDWHLLHYPTRALGGVGLILVEATAVEPLGRISPYDLGIWSEDHLPGLKELARRIREAGAVPGIQLAHAGRKAGTARPWEGGKPLGWRVVGPSPIPFDEGYPVPEPLDEAGMERILQAFVEGARRALRAGFQVIELHMAHGYLLSSFLSPLSNQRTDAYGGSLENRMRFPLQVAQAVREVVPRELPLFVRVSATDWGEGGWSLEDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPFADAVRKRVGLRTGAVGLITTPEQAETLLQAGSADLVLLGRVLLRDPYFPLRAAKALGVAPEVPPQYQRGF 349
                                    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       321       331       341        

Chain C from PDB  Type:PROTEIN  Length:348
 aligned with B0JDW3_THESC | B0JDW3 from UniProtKB/TrEMBL  Length:349

    Alignment length:348
                                    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       321       331       341        
         B0JDW3_THESC     2 ALLFTPLELGGLRLKNRLAMSPMCQYSATLEGEVTDWHLLHYPTRALGGVGLILVEATAVEPLGRISPYDLGIWSEDHLPGLKELARRIREAGAVPGIQLAHAGRKAGTARPWEGGKPLGWRVVGPSPIPFDEGYPVPEPLDEAGMERILQAFVEGARRALRAGFQVIELHMAHGYLLSSFLSPLSNQRTDAYGGSLENRMRFPLQVAQAVREVVPRELPLFVRVSATDWGEGGWSLEDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPFADAVRKRVGLRTGAVGLITTPEQAETLLQAGSADLVLLGRVLLRDPYFPLRAAKALGVAPEVPPQYQRGF 349
               SCOP domains d3hf3c_ C: automated matches                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.eee..eee...eee..............hhhhhhhhhhhhhh...eeeeeeee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh...hhhhh........ee.............ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhh..eeee....hhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhh......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hf3 C   2 ALLFTPLELGGLRLKNRLAMSPMCQYSATLEGEVTDWHLLHYPTRALGGVGLILVEATAVEPLGRISPYDLGIWSEDHLPGLKELARRIREAGAVPGIQLAHAGRKAGTARPWEGGKPLGWRVVGPSPIPFDEGYPVPEPLDEAGMERILQAFVEGARRALRAGFQVIELHMAHGYLLSSFLSPLSNQRTDAYGGSLENRMRFPLQVAQAVREVVPRELPLFVRVSATDWGEGGWSLEDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPFADAVRKRVGLRTGAVGLITTPEQAETLLQAGSADLVLLGRVLLRDPYFPLRAAKALGVAPEVPPQYQRGF 349
                                    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       321       331       341        

Chain D from PDB  Type:PROTEIN  Length:348
 aligned with B0JDW3_THESC | B0JDW3 from UniProtKB/TrEMBL  Length:349

    Alignment length:348
                                    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       321       331       341        
         B0JDW3_THESC     2 ALLFTPLELGGLRLKNRLAMSPMCQYSATLEGEVTDWHLLHYPTRALGGVGLILVEATAVEPLGRISPYDLGIWSEDHLPGLKELARRIREAGAVPGIQLAHAGRKAGTARPWEGGKPLGWRVVGPSPIPFDEGYPVPEPLDEAGMERILQAFVEGARRALRAGFQVIELHMAHGYLLSSFLSPLSNQRTDAYGGSLENRMRFPLQVAQAVREVVPRELPLFVRVSATDWGEGGWSLEDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPFADAVRKRVGLRTGAVGLITTPEQAETLLQAGSADLVLLGRVLLRDPYFPLRAAKALGVAPEVPPQYQRGF 349
               SCOP domains d3hf3d_ D: automated matches                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.eee..eee...eee..............hhhhhhhhhhhhhh...eeeeeeee.hhhhh.....ee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh...hhhhh........ee.............ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhh..eee.....hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhhh......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hf3 D   2 ALLFTPLELGGLRLKNRLAMSPMCQYSATLEGEVTDWHLLHYPTRALGGVGLILVEATAVEPLGRISPYDLGIWSEDHLPGLKELARRIREAGAVPGIQLAHAGRKAGTARPWEGGKPLGWRVVGPSPIPFDEGYPVPEPLDEAGMERILQAFVEGARRALRAGFQVIELHMAHGYLLSSFLSPLSNQRTDAYGGSLENRMRFPLQVAQAVREVVPRELPLFVRVSATDWGEGGWSLEDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPFADAVRKRVGLRTGAVGLITTPEQAETLLQAGSADLVLLGRVLLRDPYFPLRAAKALGVAPEVPPQYQRGF 349
                                    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       321       331       341        

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HF3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HF3)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (B0JDW3_THESC | B0JDW3)
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: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: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
        B0JDW3_THESC | B0JDW33hgj

(-) Related Entries Specified in the PDB File

3hgj