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(-) Description

Title :  CRYSTAL STRUCTURE DETERMINATION AT ROOM TEMPERATURE OF A LACCASE FROM TRAMETES VERSICOLOR IN ITS OXIDISED FORM CONTAINING A FULL COMPLEMENT OF COPPER IONS
 
Authors :  T. Choinowski, M. Antorini, K. Piontek
Date :  23 Apr 02  (Deposition) - 22 Aug 02  (Release) - 07 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Laccase, Oxidoreductase, Diphenol Oxidase, Lignin Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Piontek, M. Antorini, T. Choinowski
Crystal Structure Of A Laccase From The Fungus Trametes Versicolor At 1. 90-A Resolution Containing A Full Complement Of Coppers.
J. Biol. Chem. V. 277 37663 2002
PubMed-ID: 12163489  |  Reference-DOI: 10.1074/JBC.M204571200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACCASE 2
    Atcc: 20869
    Chains: A
    EC Number: 1.10.3.2
    Organism Common: WHITE-ROT FUNGUS
    Organism Scientific: TRAMETES VERSICOLOR
    Organism Taxid: 5325
    Synonym: BENZENEDIOL:OXYGEN OXIDOREDUCTASE, URISHIOL OXIDASE, DIPHENOL OXIDASE, LACCASE I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION
2IPA2Ligand/IonISOPROPYL ALCOHOL
3NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:66 , HIS A:109 , HIS A:454 , HOH A:2516BINDING SITE FOR RESIDUE CU A1500
02AC2SOFTWAREHIS A:111 , HIS A:398 , HIS A:400 , HIS A:452 , HOH A:2516BINDING SITE FOR RESIDUE CU A1501
03AC3SOFTWAREHIS A:64 , HIS A:66 , HIS A:398 , HIS A:400 , HOH A:2107BINDING SITE FOR RESIDUE CU A1502
04AC4SOFTWAREHIS A:395 , CYS A:453 , HIS A:458 , PHE A:463BINDING SITE FOR RESIDUE CU A1503
05AC5SOFTWAREHOH A:2003 , HOH A:2589 , HOH A:2590BINDING SITE FOR RESIDUE IPA A1513
06AC6SOFTWAREARG A:161 , ASN A:336 , GLU A:460 , HOH A:2419 , HOH A:2423BINDING SITE FOR RESIDUE IPA A1514
07AC7SOFTWAREARG A:22 , ASP A:23 , ASN A:54 , MET A:57 , HIS A:153 , THR A:154 , ALA A:155 , HOH A:2568 , HOH A:2570 , HOH A:2571 , HOH A:2572 , HOH A:2573 , HOH A:2574 , HOH A:2575 , HOH A:2576BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 54 RESIDUES 1504 TO 1505
08AC8SOFTWAREGLY A:215 , ASN A:217 , VAL A:297 , HOH A:2302 , HOH A:2577BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 217 RESIDUES 1506 TO 1507
09AC9SOFTWAREASN A:249 , ASN A:251 , HOH A:2578 , HOH A:2579 , HOH A:2580BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 251 RESIDUES 1508 TO 1508
10BC1SOFTWAREASN A:333 , THR A:335 , ASN A:336 , PHE A:338 , HOH A:2581 , HOH A:2582 , HOH A:2584BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 333 RESIDUES 1509 TO 1509
11BC2SOFTWAREASN A:340 , ASN A:341BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 341 RESIDUES 1512 TO 1512
12BC3SOFTWAREASN A:327 , THR A:383 , ASN A:436 , HOH A:2411 , HOH A:2585 , HOH A:2587 , HOH A:2588BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 436 RESIDUES 1510 TO 1511

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:85 -A:488
2A:117 -A:205

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:3 -Pro A:4
2Phe A:31 -Pro A:32
3Leu A:366 -Pro A:367
4Ala A:393 -Pro A:394

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GYC)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTICOPPER_OXIDASE1PS00079 Multicopper oxidases signature 1.LAC2_TRAVE124-144  1A:104-124

(-) Exons   (0, 0)

(no "Exon" information available for 1GYC)

(-) 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:499
 aligned with LAC2_TRAVE | Q12718 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:499
                                    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         
           LAC2_TRAVE    21 AIGPVASLVVANAPVSPDGFLRDAIVVNGVVPSPLITGKKGDRFQLNVDDTLTNHSMLKSTSIHWHGFFQAGTNWADGPAFVNQCPIASGHSFLYDFHVPDQAGTFWYHSHLSTQYCDGLRGPFVVYDPKDPHASRYDVDNESTVITLTDWYHTAARLGPRFPLGADATLINGLGRSASTPTAALAVINVQHGKRYRFRLVSISCDPNYTFSIDGHNLTVIEVDGINSQPLLVDSIQIFAAQRYSFVLNANQTVGNYWVRANPNFGTVGFAGGINSAILRYQGAPVAEPTTTQTTSVIPLIETNLHPLARMPVPGSPTPGGVDKALNLAFNFNGTNFFINNATFTPPTVPVLLQILSGAQTAQDLLPAGSVYPLPAHSTIEITLPATALAPGAPHPFHLHGHAFAVVRSAGSTTYNYNDPIFRDVVSTGTPAAGDNVTIRFQTDNPGPWFLHCHIDFHLDAGFAIVFAEDVADVKAANPVPKAWSDLCPIYDGLSEANQ 519
               SCOP domains d1gyca1 A:1-130 Laccase                                                                                                           d1gyca2 A:131-300 Laccase                                                                                                                                                 d1gyca3 A:301-499 Laccase                                                                                                                                                                               SCOP domains
               CATH domains 1gycA01 A:1-132 Cupredoxins -  blue copper proteins                                                                                 1gycA02 A:133-309 Cupredoxins -  blue copper proteins                                                                                                                            1gycA03 A:310-499 Cupredoxins -  blue copper proteins                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee......eeeeee........eee....eeeeeeee...hhhhh.....eee......hhhhh.............eeeeeeee.....eeeeee....hhhhhh.eeeeee......hhhhh...hhh.eeeeeee................eeee...............eeee....eeeeeeee......eeeee....eeeeee..eeeeeeee..eee....eeeeeee......eeeeeeee......hhhhh.eeeeee...................hhhhh..................ee....eee....eee..........hhhhhhhh.............eeee....eee..ee..........eeee....eeeee.............ee.eee..hhhhh.eeeeeee....eeeeeee.hhhhhhh..eeeeee...hhhhhh.......hhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gyc A   1 AIGPAASLVVANAPVSPDGFLRDAIVVNGVFPSPLITGKKGDRFQLNVVDTLTNHTMLKSTSIHWHGFFQAGTNWADGPAFVNQCPIASGHSFLYDFHVPDQAGTFWYHSHLSTQYCDGLRGPFVVYDPKDPHASRYDVDNESTVITLTDWYHTAARLGPRFPLGADATLINGLGRSASTPTAALAVINVQHGKRYRFRLVSISCDPNYTFSIDGHNLTVIEVDGINSQPLLVDSIQIFAAQRYSFVLNANQTVGNYWIRANPNFGTVGFAGGINSAILRYQGAPVAEPTTTQTTSVIPLIETNLHPLARMPVPGSPTPGGVDKALNLAFNFNGTNFFINNASFTPPTVPVLLQILSGAQTAQDLLPAGSVYPLPAHSTIEITLPATALAPGAPHPFHLHGHAFAVVRSAGSTTYNYNDPIFRDVVSTGTPAAGDNVTIRFQTDNPGPWFLHCHIDFHLEAGFAIVFAEDVADVKAANPVPKAWSDLCPIYDGLSEANQ 499
                                    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
   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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GYC)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LAC2_TRAVE | Q12718)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0052716    hydroquinone:oxygen oxidoreductase activity    Catalysis of the reaction: 4 hydroquinone + O2 = 4 benzosemiquinone + 4 H2O.
    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:0046274    lignin catabolic process    The chemical reactions and pathways resulting in the breakdown of lignins, a class of polymers of phenylpropanoid units.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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