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(-) Description

Title :  X-RAY CRYSTAL ANALYSIS OF BILIRUBIN OXIDASE FROM MYROTHECIUM VERRUCARIA AT 2.3 ANGSTROM RESOLUTION USING A TWIN CRYSTAL
 
Authors :  K. Mizutani, M. Toyoda, K. Sagara, N. Takahashi, A. Sato, Y. Kamitaka, S. Tsujimura, Y. Nakanishi, T. Sugiura, S. Yamaguchi, K. Kano, B. Mika
Date :  10 Dec 09  (Deposition) - 18 Aug 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bilirubin Oxidase, Cleavage On Pair Of Basic Residues, Glycoprotein, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Mizutani, M. Toyoda, K. Sagara, N. Takahashi, A. Sato, Y. Kamitaka, S. Tsujimura, Y. Nakanishi, T. Sugiura, S. Yamaguchi, K. Kano, B. Mikami
X-Ray Analysis Of Bilirubin Oxidase From Myrothecium Verrucaria At 2. 3 A Resolution Using A Twinned Crystal
Acta Crystallogr. , Sect. F V. 66 765 2010
PubMed-ID: 20606269  |  Reference-DOI: 10.1107/S1744309110018828

(-) Compounds

Molecule 1 - BILIRUBIN OXIDASE
    Chains: A, B
    EC Number: 1.3.3.5
    Organism Scientific: MYROTHECIUM VERRUCARIA
    Organism Taxid: 5532

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CU8Ligand/IonCOPPER (II) ION
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CU-1Ligand/IonCOPPER (II) ION
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CU-1Ligand/IonCOPPER (II) ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG-1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:452 , ASN A:472 , THR A:474 , VAL A:475 , HOH A:544 , HOH A:571 , NAG A:602BINDING SITE FOR RESIDUE NAG A 601
02AC2SOFTWARETHR A:484 , NAG A:601 , BMA A:603BINDING SITE FOR RESIDUE NAG A 602
03AC3SOFTWARENAG A:602BINDING SITE FOR RESIDUE BMA A 603
04AC4SOFTWAREASN A:482 , GLN A:495 , NAG A:612BINDING SITE FOR RESIDUE NDG A 611
05AC5SOFTWARENDG A:611BINDING SITE FOR RESIDUE NAG A 612
06AC6SOFTWAREHIS A:136 , HIS A:403 , HIS A:456 , HOH A:662BINDING SITE FOR RESIDUE CU A 701
07AC7SOFTWAREHIS A:96 , TRP A:132 , HIS A:134 , HIS A:458 , HOH A:662BINDING SITE FOR RESIDUE CU A 702
08AC8SOFTWAREHIS A:94 , HIS A:96 , HIS A:401 , HIS A:403 , HOH A:563BINDING SITE FOR RESIDUE CU A 703
09AC9SOFTWARETHR A:397 , HIS A:398 , CYS A:457 , HIS A:462 , MET A:467BINDING SITE FOR RESIDUE CU A 704
10BC1SOFTWAREASN B:472 , THR B:474 , VAL B:475 , NAG B:602BINDING SITE FOR RESIDUE NAG B 601
11BC2SOFTWAREALA B:483 , THR B:484 , NAG B:601 , BMA B:603BINDING SITE FOR RESIDUE NAG B 602
12BC3SOFTWAREHOH B:568 , NAG B:602 , HOH B:674BINDING SITE FOR RESIDUE BMA B 603
13BC4SOFTWAREASN B:482 , GLN B:495 , ALA B:496 , NAG B:612BINDING SITE FOR RESIDUE NAG B 611
14BC5SOFTWARENAG B:611BINDING SITE FOR RESIDUE NAG B 612
15BC6SOFTWAREHIS B:136 , HIS B:403 , HIS B:456 , HOH B:713BINDING SITE FOR RESIDUE CU B 701
16BC7SOFTWAREHIS B:96 , TRP B:132 , HIS B:134 , HIS B:458 , HOH B:713BINDING SITE FOR RESIDUE CU B 702
17BC8SOFTWAREHIS B:94 , HIS B:96 , HIS B:401 , HIS B:403BINDING SITE FOR RESIDUE CU B 703
18BC9SOFTWAREHIS B:398 , CYS B:457 , HIS B:462 , MET B:467BINDING SITE FOR RESIDUE CU B 704

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser A:66 -Pro A:67
2Pro A:489 -Met A:490
3Ala A:496 -Arg A:497
4Ser B:66 -Pro B:67
5Glu B:491 -Glu B:492

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ABG)

(-) 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:508
 aligned with BLRO_MYRVE | Q12737 from UniProtKB/Swiss-Prot  Length:572

    Alignment length:508
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538        
           BLRO_MYRVE    39 VAQISPQYPMFTVPLPIPPVKQPRLTVTNPVNGQEIWYYEVEIKPFTHQVYPDLGSADLVGYDGMSPGPTFQVPRGVETVVRFINNAEAPNSVHLHGSFSRAAFDGWAEDITEPGSFKDYYYPNRQSARTLWYHDHAMHITAENAYRGQAGLYMLTDPAEDALNLPSGYGEFDIPMILTSKQYTANGNLVTTNGELNSFWGDVIHVNGQPWPFKNVEPRKYRFRFLDAAVSRSFGLYFADTDAIDTRLPFKVIASDSGLLEHPADTSLLYISMAERYEVVFDFSDYAGKTIELRNLGGSIGGIGTDTDYDNTDKVMRFVVADDTTQPDTSVVPANLRDVPFPSPTTNTPRQFRFGRTGPTWTINGVAFADVQNRLLANVPVGTVERWELINAGNGWTHPIHIHLVDFKVISRTSGNNARTVMPYESGLKDVVWLGRRETVVVEAHYAPFPGVYMFHCHNLIHEDHDMMAAFNATVLPDYGYNATVFVDPMEELWQARPYELGEFQAQS 546
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................eeeeeeee..ee........ee..ee.....eeeeeee....eeeeeee.......eeee.......................eee.......eeeeee....hhhhhhhh..eeeeeee...........hhhhhh..eeeeee.....................eeee..ee.........eeeeeeee......eeeee...........eeeeee..eeeeeeeee..eee....eeeeeee.......eeeee...................eeeeee..............................eeee........................ee....eeeeeeee........eee....eeeeee..........hhhhh...ee.....eeeeeeee.....eeeeeee.hhhhhhh..eeeeee................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3abg A   1 VAQISPQYPMFTVPLPIPPVKQPRLTVTNPVNGQEIWYYEVEIKPFTHQVYPDLGSADLVGYDGMSPGPTFQVPRGVETVVRFINNAEAPNSVHLHGSFSRAAFDGWAEDITEPGSFKDYYYPNRQSARTLWYHDHAMHITAENAYRGQAGLYMLTDPAEDALNLPSGYGEFDIPMILTSKQYTANGNLVTTNGELNSFWGDVIHVNGQPWPFKNVEPRKYRFRFLDAAVSRSFGLYFADTDAIDTRLPFKVIASDSGLLEHPADTSLLYISMAERYEVVFDFSDYAGKTIELRNLGGSIGGIGTDTDYDNTDKVMRFVVADDTTQPDTSVVPANLRDVPFPSPTTNTPRQFRFGRTGPTWTINGVAFADVQNRLLANVPVGTVERWELINAGNGWTHPIHIHLVDFKVISRTSGNNARTVMPYESGLKDVVWLGRRETVVVEAHYAPFPGVYMFHCHNLIHEDHDMMAAFNATVLPDYGYNATVFVDPMEELWQARPYELGEFQAQS 508
                                    10        20        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        


Chain B from PDB  Type:PROTEIN  Length:518
 aligned with BLRO_MYRVE | Q12737 from UniProtKB/Swiss-Prot  Length:572

    Alignment length:518
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548        
           BLRO_MYRVE    39 VAQISPQYPMFTVPLPIPPVKQPRLTVTNPVNGQEIWYYEVEIKPFTHQVYPDLGSADLVGYDGMSPGPTFQVPRGVETVVRFINNAEAPNSVHLHGSFSRAAFDGWAEDITEPGSFKDYYYPNRQSARTLWYHDHAMHITAENAYRGQAGLYMLTDPAEDALNLPSGYGEFDIPMILTSKQYTANGNLVTTNGELNSFWGDVIHVNGQPWPFKNVEPRKYRFRFLDAAVSRSFGLYFADTDAIDTRLPFKVIASDSGLLEHPADTSLLYISMAERYEVVFDFSDYAGKTIELRNLGGSIGGIGTDTDYDNTDKVMRFVVADDTTQPDTSVVPANLRDVPFPSPTTNTPRQFRFGRTGPTWTINGVAFADVQNRLLANVPVGTVERWELINAGNGWTHPIHIHLVDFKVISRTSGNNARTVMPYESGLKDVVWLGRRETVVVEAHYAPFPGVYMFHCHNLIHEDHDMMAAFNATVLPDYGYNATVFVDPMEELWQARPYELGEFQAQSGQFSVQAVTE 556
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................................eeeeeee................ee..........ee....eeeeeee.......eeee.......................eee.......eeeeee....hhhhhhhh..eeeeeee..................eeeeeee.....................eeee..ee...........eeeeee......eeeee...........eeeee....eeeeeeee..eee......eee.........ee.ee.......................ee..............................eeee........................eee...eeeeeee.......eeeee....eeeeee..........hhhhh...eeee....eeeeeee.....eeeeeee.hhhhhhh..eeeeeee.......hhhhh................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3abg B   1 VAQISPQYPMFTVPLPIPPVKQPRLTVTNPVNGQEIWYYEVEIKPFTHQVYPDLGSADLVGYDGMSPGPTFQVPRGVETVVRFINNAEAPNSVHLHGSFSRAAFDGWAEDITEPGSFKDYYYPNRQSARTLWYHDHAMHITAENAYRGQAGLYMLTDPAEDALNLPSGYGEFDIPMILTSKQYTANGNLVTTNGELNSFWGDVIHVNGQPWPFKNVEPRKYRFRFLDAAVSRSFGLYFADTDAIDTRLPFKVIASDSGLLEHPADTSLLYISMAERYEVVFDFSDYAGKTIELRNLGGSIGGIGTDTDYDNTDKVMRFVVADDTTQPDTSVVPANLRDVPFPSPTTNTPRQFRFGRTGPTWTINGVAFADVQNRLLANVPVGTVERWELINAGNGWTHPIHIHLVDFKVISRTSGNNARTVMPYESGLKDVVWLGRRETVVVEAHYAPFPGVYMFHCHNLIHEDHDMMAAFNATVLPDYGYNATVFVDPMEELWQARPYELGEFQAQSGQFSVQAVTE 518
                                    10        20        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
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLRO_MYRVE | Q12737)
molecular function
    GO:0047705    bilirubin oxidase activity    Catalysis of the reaction: 2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O.
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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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        BLRO_MYRVE | Q12737: 2xll

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