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(-) Description

Title :  STRUCTURE OF RIGIDOPORUS LIGNOSUS LACCASE FROM HEMIHEDRALLY TWINNED CRYSTALS
 
Authors :  M. Rizzi, S. Garavaglia, F. Palmieri, A. Cambria
Date :  02 Apr 04  (Deposition) - 16 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Multicopper Blue Oxidase, Oxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Garavaglia, M. T. Cambria, M. Miglio, S. Ragusa, V. Iacobazzi, F. Palmieri, C. D'Ambrosio, A. Scaloni, M. Rizzi
The Structure Of Rigidoporus Lignosus Laccase Containing A Full Complement Of Copper Ions, Reveals An Asymmetrical Arrangement For The T3 Copper Pair
J. Mol. Biol. V. 342 1519 2004
PubMed-ID: 15364578  |  Reference-DOI: 10.1016/J.JMB.2004.07.100
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACCASE
    Atcc: AJ609490
    Chains: A
    EC Number: 1.10.3.2
    Organism Scientific: RIGIDOPORUS LIGNOSUS
    Organism Taxid: 219653

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:66 , TRP A:107 , HIS A:109 , HIS A:453BINDING SITE FOR RESIDUE CU A1500
2AC2SOFTWAREHIS A:111 , HIS A:401 , HIS A:451 , HOH A:2071BINDING SITE FOR RESIDUE CU A1501
3AC3SOFTWAREHIS A:64 , HIS A:66 , HIS A:399 , HIS A:401 , HOH A:2018 , HOH A:2071BINDING SITE FOR RESIDUE CU A1502
4AC4SOFTWAREHIS A:396 , CYS A:452 , ILE A:454 , HIS A:457 , LEU A:462BINDING SITE FOR RESIDUE CU A1503

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:117 -A:210

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:372 -Pro A:373

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V10)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V10)

(-) Exons   (0, 0)

(no "Exon" information available for 1V10)

(-) 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:487
 aligned with Q6H9H7_9APHY | Q6H9H7 from UniProtKB/TrEMBL  Length:521

    Alignment length:494
                                    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       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511    
         Q6H9H7_9APHY    22 ATVALDLHILNANLDPDGTGARSAVTAEGTTIAPLITGNIDDRFQINVIDQLTDANMRRATSIHWHGFFQAGTTEMDGPAFVNQCPIIPNESFVYDFVVPGQAGTYWYHSHLSTQYCDGLRGAFVVYDPNDPHLSLYDVDDASTVITIADWYHSLSTVLFPNPNKAPPAPDTTLINGLGRNSANPSAGQLAVVSVQSGKRYRFRIVSTSCFPNYAFSIDGHRMTVIEVDGVSHQPLTVDSLTIFAGQRYSVVVEANQAVGNYWIRANPSNGRNGFTGGINSAIFRYEGAAVAEPTTSQNSGTALNEANLIPLINPGAPGNPVPGGADINLNLRIGRNATTADFTINGAPFIPPTVPVLLQILSGVTNPNDLLPGGAVISLPANQVIEISIPGGGNHPFHLHGHNFDVVRTPGSSVYNYVNPVRRDVVSIGGGGDNVTFRFVTDNPGPWFLHCHIDWHLEAGLAVVFAEDIPNIPIANAISPAWDDLCPKYNANN 515
               SCOP domains d1v10a1 A:1-136 Laccase                                                                                                                 d1v10a2 A:137-304 Lac       case                                                                                                                                        d1v10a3 A:305-494 Laccase                                                                                                                                                                      SCOP domains
               CATH domains 1v10A01 A:1-129 Cupredoxins -  blue copper proteins                                                                              1v10A02 A:130-313 Cupredoxin       s -  blue copper proteins                                                                                                                            1v10A03 A:314-494 Cupredoxins -  blue copper proteins                                                                                                                                 CATH domains
               Pfam domains -------Cu-oxidase_3-1v10A03 A:8-131                                                                                                ----------Cu-oxidase-1v10A       01 A:142-289                                                                                                                 ------------------------------------------------------------Cu-oxidase_2-1v10A02 A:350-472                                                                                             ---------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee.......eeeeee........eeee...eeeeeeee............eeee......hhhhh.............eeeeeeee.....eeeeeee...hhhhhh.eeeeeee.....hhhhh...hhh.eeeeeee......-------.......eeee........hhhhh...eeee....eeeeeeee......eeeee....eeeeee..eeeeeeee..eee....eeeeeee......eeeeeeee......hhhhh.eeeeee..................hhhhh..................eeee..ee........ee..........hhhhhhhhh..hhhhh.....eeee....eeeeeee.....eeee....eeeee.............ee.eee......eeeeeee....eeeeeee.hhhhhh...eeeeee...hhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v10 A   1 ATVALDLHILNANLDPDGTGARSAVTAEGTTIAPLITGNIDDRFQINVIDQLTDANMRRATSIHWHGFFQAGTTEMDGPAFVNQCPIIPNESFVYDFVVPGQAGTYWYHSHLSTQYCDGLRGAFVVYDPNDPHLSLYDVDDASTVITIADWYHSLST-------KAPPAPDTTLINGLGRNSANPSAGQLAVVSVQSGKRYRFRIVSTSCFPNYAFSIDGHRMTVIEVDGVSHQPLTVDSLTIFAGQRYSVVVEANQAVGNYWIRANPSNGRNGFTGGINSAIFRYQGAAVAEPTTSQNSGTALNEANLIPLINPGAPGNPVPGGADINLNLRIGRNATTADFTINGAPFIPPTVPVLLQILSGVTNPNDLLPGGAVISLPANQVIEISIPGGGNHPFHLHGHNFDVVRTPGSSVYNYVNPVRRDVVSIGGGGDNVTFRFVTDNPGPWFLHCHIDWHLEAGLAVVFAEDIPNIPIANAISPAWDDLCPKYNANN 494
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |  -    |  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    
                                                                                                                                                                                      157     165
   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  (1, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6H9H7_9APHY | Q6H9H7)
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: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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