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(-) Description

Title :  STRUCTURE OF BERBERINE BRIDGE ENZYME IN COMPLEX WITH (S)-RETICULINE
 
Authors :  A. Winkler, A. Lyskowski, P. Macheroux, K. Gruber
Date :  08 May 08  (Deposition) - 28 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Bi-Covalent Flavinylation, N-Glycosylation, Substrate Complex, Alakloid Biosynthesis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Winkler, A. Lyskowski, S. Riedl, M. Puhl, T. M. Kutchan, P. Macheroux, K. Gruber
A Concerted Mechanism For Berberine Bridge Enzyme
Nat. Chem. Biol. V. 4 739 2008
PubMed-ID: 18953357  |  Reference-DOI: 10.1038/NCHEMBIO.123

(-) Compounds

Molecule 1 - BERBERINE BRIDGE-FORMING ENZYME
    Chains: A
    EC Number: 1.21.3.3
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZA
    Expression System Strain: KM71H
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: BBE1
    Organism Common: CALIFORNIA POPPY
    Organism Scientific: ESCHSCHOLZIA CALIFORNICA
    Organism Taxid: 3467
    Synonym: BBE;
TETRAHYDROPROTOBERBERINE SYNTHASE;
RETICULINE OXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4REN1Ligand/Ion(S)-RETICULINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:38 , PHE A:53 , LEU A:76 , ASN A:124 , NAG A:602BINDING SITE FOR RESIDUE NAG A 601
2AC2SOFTWAREARG A:52 , LEU A:56 , MET A:123 , PHE A:348 , NAG A:601 , MAN A:603BINDING SITE FOR RESIDUE NAG A 602
3AC3SOFTWARENAG A:602 , MAN A:604 , MAN A:605BINDING SITE FOR RESIDUE MAN A 603
4AC4SOFTWAREMAN A:603 , MAN A:605BINDING SITE FOR RESIDUE MAN A 604
5AC5SOFTWARELEU A:28 , THR A:32 , HIS A:39 , THR A:303 , MAN A:603 , MAN A:604 , MAN A:606BINDING SITE FOR RESIDUE MAN A 605
6AC6SOFTWAREASN A:25 , SER A:29 , THR A:32 , LEU A:301 , MAN A:605BINDING SITE FOR RESIDUE MAN A 606
7AC7SOFTWAREASN A:471 , VAL A:474BINDING SITE FOR RESIDUE NAG A 607
8AC8SOFTWARELEU A:99 , ARG A:100 , SER A:101 , GLY A:102 , GLY A:103 , HIS A:104 , SER A:105 , TYR A:106 , LEU A:109 , SER A:110 , LEU A:122 , SER A:141 , GLY A:164 , TRP A:165 , CYS A:166 , VAL A:169 , GLY A:170 , GLY A:173 , HIS A:174 , PHE A:180 , GLY A:225 , GLY A:226 , GLY A:229 , ILE A:231 , TYR A:456 , ASN A:458 , HIS A:459 , REN A:801 , HOH A:910BINDING SITE FOR RESIDUE FAD A 600
9AC9SOFTWARETYR A:106 , TRP A:165 , LEU A:282 , LEU A:295 , ASP A:352 , ARG A:354 , PHE A:356 , ALA A:388 , ASN A:390 , GLU A:417 , ALA A:421 , FAD A:600BINDING SITE FOR RESIDUE REN A 801

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:30 -A:89

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:451 -Pro A:452

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D2D)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_PCMHPS51387 PCMH-type FAD-binding domain profile.RETO_ESCCA67-241  1A:67-241
2OX2_COVAL_FADPS00862 Oxygen oxidoreductases covalent FAD-binding site.RETO_ESCCA71-104  1A:71-104

(-) Exons   (0, 0)

(no "Exon" information available for 3D2D)

(-) 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:500
 aligned with RETO_ESCCA | P30986 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:500
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520
           RETO_ESCCA    21 ALGGNDLLSCLTFNGVRNHTVFSADSDSDFNRFLHLSIQNPLFQNSLISKPSAIILPGSKEELSNTIRCIRKGSWTIRLRSGGHSYEGLSYTSDTPFILIDLMNLNRVSIDLESETAWVESGSTLGELYYAITESSSKLGFTAGWCPTVGTGGHISGGGFGMMSRKYGLAADNVVDAILIDANGAILDRQAMGEDVFWAIRGGGGGVWGAIYAWKIKLLPVPEKVTVFRVTKNVAIDEATSLLHKWQFVAEELEEDFTLSVLGGADEKQVWLTMLGFHFGLKTVAKSTFDLLFPELGLVEEDYLEMSWGESFAYLAGLETVSQLNNRFLKFDERAFKTKVDLTKEPLPSKAFYGLLERLSKEPNGFIALNGFGGQMSKISSDFTPFPHRSGTRLMVEYIVAWNQSEQKKKTEFLDWLEKVYEFMKPFVSKNPRLGYVNHIDLDLGGIDWGNKTVVNNAIEISRSWGESYFLSNYERLIRAKTLIDPNNVFNHPQSIPPMA 520
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh....eee......hhhhhhhh....hhhhh........eee...hhhhhhhhhhhhhh...eeeee................eeeee......eeee....eeeee...hhhhhhhhhhhhh..ee.........hhhhhhhhh....hhhhhh.hhh.eeeeeee.....eehhhhhhhhhhhhh.........eeeeeeee.ee....eeeeeeeeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhh.hhhhheeehhhhhhhhhh...hhhhhhh........eeeeeeee.....hhhhhhhhhhhhhhh..eeeeeee.hhhhhh...............eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------FAD_PCMH  PDB: A:67-241 UniProt: 67-241                                                                                                                                        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------OX2_COVAL_FAD  PDB: A:71-104      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d2d A  21 AEAGNDLLSCLTFNGVRNHTVFSADSDSDFNRFLHLSIQNPLFQNSLISKPSAIILPGSKEELSNTIRCIRKGSWTIRLRSGGHSYEGLSYTSDTPFILIDLMNLNRVSIDLESETAWVESGSTLGELYYAITESSSKLGFTAGWCPTVGTGGHISGGGFGMMSRKYGLAADNVVDAILIDANGAILDRQAMGEDVFWAIRGGGGGVWGAIYAWKIKLLPVPEKVTVFRVTKNVAIDEATSLLHKWQFVAEELEEDFTLSVLGGADEKQVWLTMLGFHFGLKTVAKSTFDLLFPELGLVEEDYLEMSWGESFAYLAGLETVSQLNNRFLKFDERAFKTKVDLTKEPLPSKAFYGLLERLSKEPNGFIALNGFGGQMSKISSDFTPFPHRSGTRLMVEYIVAWNQSEQKKKTEFLDWLEKVYEFMKPFVSKNPRLGYVNHIDLDLGGIDWGNKTVVNNAIEISRSWGESYFLSNYERLIRAKTLIDPNNVFNHPQSIPPMA 520
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3D2D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D2D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D2D)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RETO_ESCCA | P30986)
molecular function
    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: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:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0050468    reticuline oxidase activity    Catalysis of the reaction: (S)-reticuline + O(2) = (S)-scoulerine + H(2)O(2) + H(+).
biological process
    GO:0009820    alkaloid metabolic process    The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
    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.
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RETO_ESCCA | P30986: 3d2h 3d2j 3fw7 3fw8 3fw9 3fwa 3gsy 4ec3 4pzf

(-) Related Entries Specified in the PDB File

3d2h STRUCTURE OF BERBERINE BRIDGE ENZYME, MONOCLINIC CRYSTAL FORM
3d2j STRUCTURE OF BERBERINE BRIDGE ENZYME, TETRAGONAL CRYSTAL FORM