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(-) Description

Title :  STRUCTURE OF BERBERINE BRIDGE ENZYME, H174A VARIANT IN COMPLEX WITH (S)-RETICULINE
 
Authors :  A. Winkler, P. Macheroux, K. Gruber
Date :  26 Mar 12  (Deposition) - 18 Jul 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  P-Cresol Methyl Hydroxylase Superfamily, Oxidoreductase, Fad, Bi- Covalent Flavinylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Wallner, A. Winkler, S. Riedl, C. Dully, S. Horvath, K. Gruber, P. Macheroux
Catalytic And Structural Role Of A Conserved Active Site Histidine In Berberine Bridge Enzyme.
Biochemistry V. 51 6139 2012
PubMed-ID: 22757961  |  Reference-DOI: 10.1021/BI300411N

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL1Ligand/IonCHLORIDE ION
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MAN3Ligand/IonALPHA-D-MANNOSE
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6REN1Ligand/Ion(S)-RETICULINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:99 , ARG A:100 , SER A:101 , GLY A:102 , GLY A:103 , HIS A:104 , SER A:105 , TYR A:106 , 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:172 , GLY A:173 , ALA A:174 , GLY A:179 , PHE A:180 , GLY A:225 , GLY A:226 , GLY A:229 , ILE A:231 , PHE A:351 , TYR A:456 , ASN A:458 , REN A:602 , HOH A:720 , HOH A:735 , HOH A:742BINDING SITE FOR RESIDUE FAD A 601
02AC2SOFTWARETYR A:106 , TRP A:165 , SER A:280 , LEU A:282 , LEU A:295 , ASP A:352 , ARG A:354 , PHE A:356 , PHE A:386 , ASN A:390 , GLU A:417 , FAD A:601BINDING SITE FOR RESIDUE REN A 602
03AC3SOFTWAREASN A:38 , LEU A:76 , ASN A:124 , NAG A:604BINDING SITE FOR RESIDUE NAG A 603
04AC4SOFTWAREARG A:52 , LEU A:56 , NAG A:603 , BMA A:605BINDING SITE FOR RESIDUE NAG A 604
05AC5SOFTWARENAG A:604 , MAN A:606 , MAN A:607BINDING SITE FOR RESIDUE BMA A 605
06AC6SOFTWAREBMA A:605 , MAN A:607 , MAN A:608BINDING SITE FOR RESIDUE MAN A 606
07AC7SOFTWARELEU A:28 , THR A:32 , HIS A:39 , THR A:303 , BMA A:605 , MAN A:606 , MAN A:608BINDING SITE FOR RESIDUE MAN A 607
08AC8SOFTWAREASN A:25 , SER A:29 , THR A:32 , LEU A:301 , MAN A:606 , MAN A:607 , HOH A:723BINDING SITE FOR RESIDUE MAN A 608
09AC9SOFTWAREASN A:471 , VAL A:474 , HOH A:747BINDING SITE FOR RESIDUE NAG A 609
10BC1SOFTWARETYR A:149 , THR A:162 , ALA A:163 , GLY A:164 , GLY A:181 , MET A:182 , PHE A:332 , HOH A:803BINDING SITE FOR RESIDUE CL A 610

(-) 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 4EC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EC3)

(-) Exons   (0, 0)

(no "Exon" information available for 4EC3)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh....eee......hhhhhhhhhh..hhhhh........eee...hhhhhhhhhhhhhh...eeeee................eeeee......eeee....eeeee...hhhhhhhhhhhhh..ee.........hhhhhhhhh....hhhhhh.hhh.eeeeeee.....eehhhhhhhhhhhhh.........eeeeeeee.ee....eeeeeeeeeehhhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhh.hhhhheeehhhhhhhhhhh...hhhhhh........eeeeeeee.....hhhhhhhhhhhhhhh..eeeeeee..hhhhhh..............eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ec3 A  21 AEAGNDLLSCLTFNGVRNHTVFSADSDSDFNRFLHLSIQNPLFQNSLISKPSAIILPGSKEELSNTIRCIRKGSWTIRLRSGGHSYEGLSYTSDTPFILIDLMNLNRVSIDLESETAWVESGSTLGELYYAITESSSKLGFTAGWCPTVGTGGAISGGGFGMMSRKYGLAADNVVDAILIDANGAILDRQAMGEDVFWAIRGGGGGVWGAIYAWKIKLLPVPEKVTVFRVTKNVAIDEATSLLHKWQFVAEELEEDFTLSVLGGADEKQVWLTMLGFHFGLKTVAKSTFDLLFPELGLVEEDYLEMSWGESFAYLAGLETVSQLNNRFLKFDERAFKTKVDLTKEPLPSKAFYGLLERLSKEPNGFIALNGFGGQMSKISSDFTPFPHRSGTRLMVEYIVAWNQSEQKKKTEFLDWLEKVYEFMKPFVSKNPRLGYVNHIDLDLGGIDWGNKTVVNNAIEISRSWGESYFLSNYERLIRAKTLIDPNNVFNHPQSIPPMA 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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  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  (0, 0)

(no "SCOP Domain" information available for 4EC3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EC3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EC3)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RETO_ESCCA | P30986: 3d2d 3d2h 3d2j 3fw7 3fw8 3fw9 3fwa 3gsy 4pzf

(-) Related Entries Specified in the PDB File

3d2d STRUCTURE OF BERBERINE BRIDGE ENZYME IN COMPLEX WITH (S)- RETICULINE
3d2j STRUCTURE OF BERBERINE BRIDGE ENZYME FROM ESCHSCHOLZIA CALIFORNICA, TETRAGONAL CRYSTAL FORM
3fw7 STRUCTURE OF BERBERINE BRIDGE ENZYME, H104A VARIANT
3fw8 STRUCTURE OF BERBERINE BRIDGE ENZYME, C166A VARIANT