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(-) Description

Title :  XENOBIOTIC REDUCTASE A - COUMARIN BOUND
 
Authors :  O. Spiegelhauer, H. Dobbek
Date :  22 Dec 09  (Deposition) - 23 Mar 10  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tim Barrel, Fmn, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Spiegelhauer, S. Mende, F. Dickert, S. H. Knauer, G. M. Ullmann, H. Dobbek
Cysteine As A Modulator Residue In The Active Site Of Xenobiotic Reductase A: A Structural, Thermodynamic And Kinetic Study
J. Mol. Biol. V. 398 66 2010
PubMed-ID: 20206186  |  Reference-DOI: 10.1016/J.JMB.2010.02.044

(-) Compounds

Molecule 1 - XENOBIOTIC REDUCTASE A
    Chains: A
    EC Number: 1.6.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: XENA
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Strain: 86

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1BU33Ligand/Ion(R,R)-2,3-BUTANEDIOL
2COU2Ligand/IonCOUMARIN
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
4SO46Ligand/IonSULFATE ION
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1BU36Ligand/Ion(R,R)-2,3-BUTANEDIOL
2COU4Ligand/IonCOUMARIN
3FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
4SO412Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:346 , ALA A:347 , SER A:348 , HOH A:1716 , HOH A:1765BINDING SITE FOR RESIDUE SO4 A 1501
02AC2SOFTWAREGLU A:6 , TYR A:8 , ARG A:18 , HOH A:1609 , HOH A:1614 , HOH A:1911BINDING SITE FOR RESIDUE SO4 A 1502
03AC3SOFTWARELYS A:295 , LEU A:296 , PRO A:297 , HOH A:1644 , HOH A:1835 , HOH A:1858 , HOH A:2013BINDING SITE FOR RESIDUE SO4 A 1503
04AC4SOFTWARETRP A:278 , GLY A:279 , PRO A:280 , TRP A:302 , HOH A:1671 , HOH A:1995 , HOH A:2042BINDING SITE FOR RESIDUE SO4 A 1504
05AC5SOFTWAREASP A:205 , ARG A:209 , ARG A:254 , HOH A:1627 , HOH A:1757 , HOH A:1775 , HOH A:1786BINDING SITE FOR RESIDUE SO4 A 1505
06AC6SOFTWAREARG A:111 , ARG A:125 , HOH A:1814BINDING SITE FOR RESIDUE SO4 A 1506
07AC7SOFTWAREPRO A:112 , ASP A:116 , HIS A:181 , ARG A:231 , SER A:266 , PHE A:269 , ALA A:301 , TRP A:302 , TRP A:358 , COU A:801 , FMN A:1401 , HOH A:1687 , HOH A:1723 , HOH A:1996BINDING SITE FOR RESIDUE BU3 A 1508
08AC8SOFTWAREPHE A:189 , SER A:190 , GLU A:191 , ARG A:240 , GLN A:243 , GLU A:247 , HOH A:1551 , HOH A:1823 , HOH A:1865BINDING SITE FOR RESIDUE BU3 A 1509
09AC9SOFTWAREPRO A:22 , PRO A:23 , MET A:24 , CYS A:25 , ALA A:57 , GLN A:99 , HIS A:178 , HIS A:181 , ARG A:231 , ALA A:301 , TRP A:302 , GLY A:303 , GLY A:325 , ARG A:326 , TRP A:358 , COU A:801 , BU3 A:1508 , HOH A:1545 , HOH A:1591 , HOH A:1954 , HOH A:2026 , HOH A:2077BINDING SITE FOR RESIDUE FMN A 1401
10BC1SOFTWARETYR A:27 , HIS A:178 , HIS A:181 , TYR A:183 , FMN A:1401 , BU3 A:1508 , HOH A:2026BINDING SITE FOR RESIDUE COU A 801
11BC2SOFTWAREMET A:28 , ARG A:47 , ALA A:91 , ALA A:92 , PRO A:352 , HOH A:1603 , HOH A:1805 , HOH A:2062BINDING SITE FOR RESIDUE COU A 802
12BC3SOFTWARETHR A:14 , LYS A:90 , GLY A:93 , SER A:94 , VAL A:95 , GLU A:173 , HOH A:1573 , HOH A:1944BINDING SITE FOR RESIDUE BU3 A 2176

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L5M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L5M)

(-) Exons   (0, 0)

(no "Exon" information available for 3L5M)

(-) 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:359
 aligned with Q3ZDM6_PSEPU | Q3ZDM6 from UniProtKB/TrEMBL  Length:363

    Alignment length:359
                                    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       351         
         Q3ZDM6_PSEPU     2 SALFEPYTLKDVTLRNRIAIPPMCQYMAEDGMINDWHHVHLAGLARGGAGLLVVEATAVAPEGRITPGCAGIWSDAHAQAFVPVVQAIKAAGSVPGIQIAHAGRKASANRPWEGDDHIAADDARGWETIAPSAIAFGAHLPKVPREMTLDDIARVKQDFVDAARRARDAGFEWIELHFAHGYLGQSFFSEHSNKRTDAYGGSFENRSRFLLETLAAVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTIPDTHIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLADPHWAYFAAKELGVEKASWTLPAPYAHWLE 360
               SCOP domains d3l5ma_ A: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -Oxidored_FMN-3l5mA01 A:3-343                                                                                                                                                                                                                                                                                                                         ----------------- Pfam domains
         Sec.struct. author hhhhh.eee..eee...eee.............hhhhhhhhhhhhhh...eeeeeeee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh...hhhhh..............ee..............ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhhhhhhhhhhhh...eeeeee...............hhhhhhhhhhhhh..eee.....hhhhhhhhhhh....eee.hhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l5m A   2 SALFEPYTLKDVTLRNRIAIPPMCQYMAEDGMINDWHHVHLAGLARGGAGLLVVEATAVAPEGRITPGCAGIWSDAHAQAFVPVVQAIKAAGSVPGIQIAHAGRKASANRPWEGDDHIAADDTRGWETIAPSAIAFGAHLPKVPREMTLDDIARVKQDFVDAARRARDAGFEWIELHFAHGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLAAVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTIPDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLADPHWAYFAAKELGVEKASWTLPAPYAHWLE 360
                                    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       351
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L5M)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q3ZDM6_PSEPU | Q3ZDM6)
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: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)

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        Q3ZDM6_PSEPU | Q3ZDM6: 3l5l 3l65 3l66 3l67 3l68 3n14 3n19 4uth 4uti 4utj 4utk 4utl 4utm

(-) Related Entries Specified in the PDB File

2h8z 3l5l 3l65 3l66 3l67 3l68