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(-) Description

Title :  TYPE-2 CU-DEPLETED FUNGUS LACCASE FROM TRAMETES HIRSUTA
 
Authors :  K. M. Polyakov, T. V. Fedorova, S. A. Kurzeev, A. N. Popov, V. S. Lamzin, O. V. Koroleva
Date :  10 Dec 10  (Deposition) - 16 Feb 11  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  4-Copper Protein, Metal-Binding, Oxidoreductase, Type-2 Cu-Depleted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Polyakov, T. V. Fedorova, S. A. Kurzeev, A. N. Popov, V. S. Lamzin, O. V. Koroleva
Crystal Structure Of T2-Depleted Fungal Laccase From Trametes Hirsuta At Low And High Dose Of Ionization Radiation.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACCASE
    Chains: A
    EC Number: 1.10.3.2
    Organism Common: WHITE-ROT FUNGUS
    Organism Scientific: TRAMETES HIRSUTA
    Organism Taxid: 5327

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CU4Ligand/IonCOPPER (II) ION
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:111 , HIS A:398 , HIS A:400 , HIS A:452 , HOH A:1411 , CU A:1502BINDING SITE FOR RESIDUE CU A 1500
02AC2SOFTWAREHIS A:64 , HIS A:66 , TRP A:107 , HIS A:109 , HIS A:454 , HOH A:1411BINDING SITE FOR RESIDUE CU A 1501
03AC3SOFTWAREHIS A:395 , CYS A:453 , ILE A:455 , HIS A:458BINDING SITE FOR RESIDUE CU A 1503
04AC4SOFTWAREHIS A:64 , HIS A:66 , HIS A:398 , HIS A:400 , HOH A:1003 , CU A:1500BINDING SITE FOR RESIDUE CU A 1502
05AC5SOFTWAREGLN A:23 , ASN A:54 , MET A:57 , ALA A:155 , LEU A:158 , HOH A:812 , HOH A:880 , HOH A:1004 , NAG A:1505BINDING SITE FOR RESIDUE NAG A 1504
06AC6SOFTWAREARG A:22 , HIS A:153 , THR A:154 , ALA A:155 , LEU A:158 , HOH A:880 , HOH A:1065 , HOH A:1355 , HOH A:1375 , HOH A:1379 , NAG A:1504 , BMA A:1512BINDING SITE FOR RESIDUE NAG A 1505
07AC7SOFTWAREPHE A:20 , HOH A:601 , HOH A:807 , HOH A:1285 , HOH A:1303 , NAG A:1505 , MAN A:1513 , MAN A:1515BINDING SITE FOR RESIDUE BMA A 1512
08AC8SOFTWAREVAL A:5 , PHE A:20 , SER A:21 , HOH A:603 , HOH A:1035 , HOH A:1036 , HOH A:1245 , BMA A:1512 , MAN A:1514 , MAN A:1520BINDING SITE FOR RESIDUE MAN A 1513
09AC9SOFTWAREPRO A:4 , ALA A:14 , SER A:21 , ASN A:39 , ASP A:42 , HOH A:615 , HOH A:807 , HOH A:1004 , HOH A:1355 , HOH A:1358 , HOH A:1376 , HOH A:1407 , MAN A:1513BINDING SITE FOR RESIDUE MAN A 1514
10BC1SOFTWAREVAL A:5 , ALA A:6 , HOH A:1283 , BMA A:1512BINDING SITE FOR RESIDUE MAN A 1515
11BC2SOFTWAREVAL A:5 , ARG A:43 , GLN A:45 , HOH A:603 , HOH A:1391 , MAN A:1513BINDING SITE FOR RESIDUE MAN A 1520
12BC3SOFTWAREGLY A:215 , ASN A:217 , GLN A:252 , LYS A:298 , HOH A:1064 , HOH A:1289 , NAG A:1507BINDING SITE FOR RESIDUE NAG A 1506
13BC4SOFTWARELYS A:157 , LEU A:158 , GLY A:159 , HOH A:1086 , HOH A:1289 , HOH A:1410 , NAG A:1506 , BMA A:1508BINDING SITE FOR RESIDUE NAG A 1507
14BC5SOFTWARELYS A:157 , HOH A:1368 , HOH A:1369 , HOH A:1410 , NAG A:1507BINDING SITE FOR RESIDUE BMA A 1508
15BC6SOFTWAREASN A:333 , SER A:335 , ASN A:336 , PHE A:338BINDING SITE FOR RESIDUE NAG A 1509
16BC7SOFTWARESER A:319 , SER A:383 , PRO A:385 , ASN A:436 , HOH A:742 , HOH A:764 , HOH A:854 , HOH A:1242 , NAG A:1511BINDING SITE FOR RESIDUE NAG A 1510
17BC8SOFTWAREASN A:327 , HOH A:853 , HOH A:1024 , NAG A:1510BINDING SITE FOR RESIDUE NAG A 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
2Thr 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 3PXL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PXL)

(-) 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 B2L9C1_TRAHI | B2L9C1 from UniProtKB/TrEMBL  Length:520

    Alignment length:499
                                    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         
         B2L9C1_TRAHI    22 AVGPVADLTITDAAVSPDGFSRQAVVVNGVTPGPLVAGNIGDRFQLNVIDNLTNHTMLKSTSIHWHGFFQHGTNWADGPAFINQCPISPGHSFLYDFQVPDQAGTFWYHSHLSTQYCDGLRGPFVVYDPNDPHASRYDVDNDDTVITLADWYHTAAKLGPRFPGGADATLINGKGRAPSDSPAELSVIKVTKGKRYRFRLVSLSCNPNHTFSIDGHNLTIIEVDSVNSQPLEVDSIQIFAAQRYSFVLDANQAVDNYWIRANPNFGNVGFDGGINSAILRYDGAPAVEPTTNQTTSVKPLNEVDLHPLVSTPVPGSPSSGGVDKAINMAFNFNGSNFFINGASFVPPTVPVLLQILSGAQTAQDLLPSGSVYVLPSNASIEISFPATAAAPGAPHPFHLHGHTFAVVRSAGSTVYNYDNPIFRDVVSTGTPAAGDNVTIRFDTNNPGPWFLHCHIDFHLEGGFAVVMAEDTPDVKAVNPVPQAWSDLCPTYDALDPNDQ 520
               SCOP domains d3pxla1 A:1-130 automated matches                                                                                                 d3pxla2 A:131-300 automated matches                                                                                                                                       d3pxla3 A:301-499 automated matches                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------Cu-oxidase_3-3pxlA03 A:9-131                                                                                               ----------Cu-oxidase-3pxlA01 A:142-284                                                                                                                   -----------------------------------------------------------Cu-oxidase_2-3pxlA02 A:344-473                                                                                                    -------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee......eeeeee........eeee...eeeeeeee...hhhhh....eeee......hhhhh..............eeeeeee.....eeeeeee...hhhhhh.eeeeeee.....hhhhh...hhh.eeeeeee................eeee...............eeee....eeeeeeee......eeeee....eeeeee..eeeeeeee..eee....eeeeeee......eeeeeeee......hhhhh.eeeeee...................hhhhh..................eeee..eee....eee..........hhhhhhhh.............eeee....eeeeeee..........eeee....eeeee.............ee.eee..hhhhh.eeeeeee....eeeeeee.hhhhhhh..eeeeee...hhhhhh..hhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pxl A   1 AVGPVADLTITDAAVSPDGFSRQAVVVNGVTPGPLVAGNIGDRFQLNVIDNLTNHTMLKSTSIHWHGFFQHGTNWADGPAFINQCPISPGHSFLYDFQVPDQAGTFWYHSHLSTQYCDGLRGPFVVYDPNDPHASRYDVDNDDTVITLADWYHTAAKLGPRFPGGADATLINGKGRAPSDSVAELSVIKVTKGKRYRFRLVSLSCNPNHTFSIDGHNLTIIEVDSVNSQPLEVDSIQIFAAQRYSFVLDANQAVDNYWIRANPNFGNVGFDGGINSAILRYDGAPAVEPTTNQTTSVKPLNEVDLHPLVSTPVPGAPSSGGVDKAINMAFNFNGSNFFINGASFVPPTVPVLLQILSGAQTAQDLLPSGSVYVLPSNASIEISFPATAAAPGAPHPFHLHGHTFAVVRSAGSTVYNYDNPIFRDVVSTGTPAAGDNVTIRFDTNNPGPWFLHCHIDFHLEGGFAVVMAEDTPDVKAVNPVPQAWSDLCPTYDALDPNDQ 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)
  - → 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  (1, 3)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 3)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B2L9C1_TRAHI | B2L9C1)
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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 Related Entries

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        B2L9C1_TRAHI | B2L9C1: 3fpx 3v9c

(-) Related Entries Specified in the PDB File

3fpx THE NATIVE FORM OF THE SAME PROTEIN.