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(-) Description

Title :  MELANOCARPUS ALBOMYCES LACCASE CRYSTAL SOAKED (20 MIN) WITH 2,6-DIMETHOXYPHENOL
 
Authors :  J. P. Kallio, N. Hakulinen, J. Rouvinen
Date :  14 Jan 09  (Deposition) - 22 Sep 09  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Laccase, Multicopper Oxidase, Complex Structure, 2, 6-Dimethoxyphenol, Oxidation Of Phenolic Compounds, Glycoprotein, Lignin Degradation, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Kallio, S. Auer, J. Janis, M. Andberg, K. Kruus, J. Rouvinen, A. Koivula, N. Hakulinen
Structure-Function Studies Of A Melanocarpus Albomyces Laccase Suggest A Pathway For Oxidation Of Phenolic Compounds.
J. Mol. Biol. V. 392 895 2009
PubMed-ID: 19563811  |  Reference-DOI: 10.1016/J.JMB.2009.06.053

(-) Compounds

Molecule 1 - LACCASE-1
    Chains: A, B
    EC Number: 1.10.3.2
    Engineered: YES
    Expression System: TRICHODERMA REESEI
    Expression System Strain: RUTC-30
    Expression System Taxid: 51453
    Gene: LAC1
    Organism Scientific: MELANOCARPUS ALBOMYCES
    Organism Taxid: 204285
    Strain: VTT D-96490

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 29)

Asymmetric/Biological Unit (5, 29)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CU8Ligand/IonCOPPER (II) ION
3KIB2Ligand/Ion2,6-DIMETHOXYBENZENE-1,4-DIOL
4NAG15Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO42Ligand/IonSULFATE ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:431 , CYS A:503 , HIS A:508BINDING SITE FOR RESIDUE CU A 601
02AC2SOFTWAREHIS A:140 , HIS A:436 , HIS A:502 , HOH A:568BINDING SITE FOR RESIDUE CU A 602
03AC3SOFTWAREHIS A:95 , HIS A:138 , HIS A:504 , HOH A:568BINDING SITE FOR RESIDUE CU A 603
04AC4SOFTWAREHIS A:93 , HIS A:434 , HIS A:436 , CL A:610BINDING SITE FOR RESIDUE CU A 604
05AC5SOFTWAREGLY A:96 , HIS A:434 , LEU A:435 , HIS A:436 , HOH A:563 , CU A:604 , HOH A:715BINDING SITE FOR RESIDUE CL A 610
06AC6SOFTWAREASN A:39 , ASN A:84 , HOH A:780 , GLU B:78 , ARG B:126BINDING SITE FOR RESIDUE NAG A 700
07AC7SOFTWARELYS A:56 , MET A:58 , THR A:87 , ASN A:88 , ASP A:181 , ASN A:550 , TYR A:552 , PRO A:553 , NAG A:711 , HOH A:750 , HOH A:786BINDING SITE FOR RESIDUE NAG A 710
08AC8SOFTWAREGLU A:55 , ASP A:182 , TYR A:552 , NAG A:710 , HOH A:721BINDING SITE FOR RESIDUE NAG A 711
09AC9SOFTWAREASN A:216 , THR A:218 , ILE A:309 , HIS A:311 , HOH A:716 , HOH A:752 , HOH A:871BINDING SITE FOR RESIDUE NAG A 720
10BC1SOFTWARETRP A:287 , ASN A:289 , HIS A:305 , ALA A:307 , GLU A:323 , NAG A:731 , HOH A:737BINDING SITE FOR RESIDUE NAG A 730
11BC2SOFTWARETRP A:287 , HIS A:305 , GLU A:323 , NAG A:730 , HOH A:816 , HOH A:874BINDING SITE FOR RESIDUE NAG A 731
12BC3SOFTWAREPRO A:355 , THR A:358 , LEU A:359 , ASN A:376 , VAL A:406 , HOH A:732BINDING SITE FOR RESIDUE NAG A 740
13BC4SOFTWAREARG A:128 , ARG A:130 , HOH A:609 , ARG B:492BINDING SITE FOR RESIDUE SO4 A 8002
14BC5SOFTWAREPRO A:192 , ALA A:297 , PHE A:371 , LEU A:429 , HIS A:508BINDING SITE FOR RESIDUE KIB A 1001
15BC6SOFTWAREHIS B:431 , CYS B:503 , HIS B:508BINDING SITE FOR RESIDUE CU B 601
16BC7SOFTWAREHIS B:140 , HIS B:436 , HIS B:502 , HOH B:617BINDING SITE FOR RESIDUE CU B 602
17BC8SOFTWAREHIS B:95 , TRP B:136 , HIS B:138 , HIS B:504 , HOH B:617BINDING SITE FOR RESIDUE CU B 603
18BC9SOFTWAREHIS B:93 , HIS B:95 , HIS B:434 , HIS B:436 , CL B:610BINDING SITE FOR RESIDUE CU B 604
19CC1SOFTWAREHIS B:93 , GLY B:96 , HIS B:434 , CU B:604 , HOH B:844BINDING SITE FOR RESIDUE CL B 610
20CC2SOFTWAREGLU A:78 , ARG A:126 , ASN B:39 , HOH B:696 , HOH B:845BINDING SITE FOR RESIDUE NAG B 700
21CC3SOFTWAREGLU B:42 , LYS B:56 , THR B:87 , ASN B:88 , ASP B:181 , ASN B:550 , TYR B:552 , HOH B:560 , HOH B:678 , NAG B:711 , HOH B:742 , HOH B:937BINDING SITE FOR RESIDUE NAG B 710
22CC4SOFTWAREGLU B:55 , ALA B:179 , ASP B:181 , ASP B:182 , TYR B:552 , HOH B:608 , NAG B:710 , HOH B:734 , HOH B:899 , HOH B:924BINDING SITE FOR RESIDUE NAG B 711
23CC5SOFTWAREASN B:216 , THR B:218 , HIS B:311 , GLY B:317 , HOH B:572 , HOH B:614BINDING SITE FOR RESIDUE NAG B 720
24CC6SOFTWAREVAL B:243 , TRP B:287 , ASN B:289 , HIS B:305 , ALA B:307 , GLU B:323 , NAG B:731 , HOH B:762BINDING SITE FOR RESIDUE NAG B 730
25CC7SOFTWARETRP B:287 , HIS B:305 , GLU B:323 , NAG B:730 , HOH B:853BINDING SITE FOR RESIDUE NAG B 731
26CC8SOFTWAREPRO B:355 , ASP B:356 , THR B:358 , ASN B:376 , HOH B:622 , HOH B:745 , HOH B:893BINDING SITE FOR RESIDUE NAG B 740
27CC9SOFTWAREPHE B:170 , ASN B:201 , VAL B:217 , HOH B:744 , HOH B:786 , HOH B:827 , HOH B:861BINDING SITE FOR RESIDUE NAG B 760
28DC1SOFTWAREARG A:492 , ARG B:128 , ARG B:130BINDING SITE FOR RESIDUE SO4 B 8001
29DC2SOFTWAREALA B:191 , PRO B:192 , ALA B:296 , ALA B:297 , LEU B:429 , HIS B:508 , HOH B:566 , HOH B:607 , HOH B:797 , HOH B:819BINDING SITE FOR RESIDUE KIB B 2001

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:114 -A:540
2A:298 -A:332
3B:4 -B:12
4B:114 -B:540
5B:298 -B:332

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:368 -Pro A:369
2Thr B:368 -Pro B:369

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FU9)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTICOPPER_OXIDASE1PS00079 Multicopper oxidases signature 1.LAC1_MELAO547-567
 		  2A:497-517
B:497-517
2MULTICOPPER_OXIDASE2PS00080 Multicopper oxidases signature 2.LAC1_MELAO552-563
 		  2A:502-513
B:502-513

(-) Exons   (0, 0)

(no "Exon" information available for 3FU9)

(-) 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:559
 aligned with LAC1_MELAO | Q70KY3 from UniProtKB/Swiss-Prot  Length:623

    Alignment length:559
                                    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       530       540       550       560       570       580       590       600         
           LAC1_MELAO    51 EPTCNTPSNRACWSDGFDINTDYEVSTPDTGVTQSYVFNLTEVDNWMGPDGVVKEKVMLINGNIMGPNIVANWGDTVEVTVINNLVTNGTSIHWHGIHQKDTNLHDGANGVTECPIPPKGGQRTYRWRARQYGTSWYHSHFSAQYGNGVVGTIQINGPASLPYDIDLGVFPITDYYYRAADDLVHFTQNNAPPFSDNVLINGTAVNPNTGEGQYANVTLTPGKRHRLRILNTSTENHFQVSLVNHTMTVIAADMVPVNAMTVDSLFLAVGQRYDVVIDASRAPDNYWFNVTFGGQAACGGSLNPHPAAIFHYAGAPGGLPTDEGTPPVDHQCLDTLDVRPVVPRSVPVNSFVKRPDNTLPVALDLTGTPLFVWKVNGSDINVDWGKPIIDYILTGNTSYPVSDNIVQVDAVDQWTYWLIENDPEGPFSLPHPMHLHGHDFLVLGRSPDVPAASQQRFVFDPAVDLARLNGDNPPRRDTTMLPAGGWLLLAFRTDNPGAWLFHCHIAWHVSGGLSVDFLERPADLRQRISQEDEDDFNRVCDEWRAYWPTNPYPKIDSGL 609
               SCOP domains d3fu9a1 A:1-162 Laccase                                                                                                                                           d3fu9a2 A:163-343 Laccase                                                                                                                                                            d3fu9a3 A:344-559 Laccase                                                                                                                                                                                                SCOP domains
               CATH domains 3fu9A01 A:1-158 Cupredoxins -  blue copper proteins                                                                                                           3fu9A02 A:159-342 Cupredoxins -  blue copper proteins                                                                                                                                   3fu9A03 A:343-559 Cupredoxins -  blue copper proteins                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..ee..............eeeeeeeeeeeeeee.....eeeeeeee........eeee...eeeeeeeee.......eeee......hhhhh...............eeeeeee....eeeeeee...hhhhhh.eeeeeee........eeeeeeeeeee...hhhhhhhhhhhh......eeee...............eeee....eeeeeeee......eeeee....eeeeee..eeeeeeee..eee....eeeeeee......eeeeeee.hhhhh.........eeeeee.............................................eeeeeee.......eeee...........hhhhhhhh..........eeee.....eeeeeeee.........eeeee....eeeeee..............hhhhhh.........ee.eeee....eeeeeee....eeeeeee.hhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 ------------------------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_---------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fu9 A   1 EPTCNTPSNRACWSDGFDINTDYEVSTPDTGVTQSYVFNLTEVDNWMGPDGVVKEKVMLINGNIMGPNIVANWGDTVEVTVINNLVTNGTSIHWHGIHQKDTNLHDGANGVTECPIPPKGGQRTYRWRARQYGTSWYHSHFSAQYGNGVVGTIQINGPASLPYDIDLGVFPITDYYYRAADDLVHFTQNNAPPFSDNVLINGTAVNPNTGEGQYANVTLTPGKRHRLRILNTSTENHFQVSLVNHTMTVIAADMVPVNAMTVDSLFLAVGQRYDVVIDASRAPDNYWFNVTFGGQAACGGSLNPHPAAIFHYAGAPGGLPTDEGTPPVDHQCLDTLDVRPVVPRSVPVNSFVKRPDNTLPVALDLTGTPLFVWKVNGSDINVDWGKPIIDYILTGNTSYPVSDNIVQVDAVDQWTYWLIENDPEGPFSLPHPMHLHGHDFLVLGRSPDVPAASQQRFVFDPAVDLARLNGDNPPRRDTTMLPAGGWLLLAFRTDNPGAWLFHCHIAWHVSGGLSVDFLERPADLRQRISQEDEDDFNRVCDEWRAYWPTNPYPKIDSGL 559
                                    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       520       530       540       550         


Chain B from PDB  Type:PROTEIN  Length:559
 aligned with LAC1_MELAO | Q70KY3 from UniProtKB/Swiss-Prot  Length:623

    Alignment length:559
                                    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       530       540       550       560       570       580       590       600         
           LAC1_MELAO    51 EPTCNTPSNRACWSDGFDINTDYEVSTPDTGVTQSYVFNLTEVDNWMGPDGVVKEKVMLINGNIMGPNIVANWGDTVEVTVINNLVTNGTSIHWHGIHQKDTNLHDGANGVTECPIPPKGGQRTYRWRARQYGTSWYHSHFSAQYGNGVVGTIQINGPASLPYDIDLGVFPITDYYYRAADDLVHFTQNNAPPFSDNVLINGTAVNPNTGEGQYANVTLTPGKRHRLRILNTSTENHFQVSLVNHTMTVIAADMVPVNAMTVDSLFLAVGQRYDVVIDASRAPDNYWFNVTFGGQAACGGSLNPHPAAIFHYAGAPGGLPTDEGTPPVDHQCLDTLDVRPVVPRSVPVNSFVKRPDNTLPVALDLTGTPLFVWKVNGSDINVDWGKPIIDYILTGNTSYPVSDNIVQVDAVDQWTYWLIENDPEGPFSLPHPMHLHGHDFLVLGRSPDVPAASQQRFVFDPAVDLARLNGDNPPRRDTTMLPAGGWLLLAFRTDNPGAWLFHCHIAWHVSGGLSVDFLERPADLRQRISQEDEDDFNRVCDEWRAYWPTNPYPKIDSGL 609
               SCOP domains d3fu9b1 B:1-162 Laccase                                                                                                                                           d3fu9b2 B:163-343 Laccase                                                                                                                                                            d3fu9b3 B:344-559 Laccase                                                                                                                                                                                                SCOP domains
               CATH domains 3fu9B01 B:1-158 Cupredoxins -  blue copper proteins                                                                                                           3fu9B02 B:159-342 Cupredoxins -  blue copper proteins                                                                                                                                   3fu9B03 B:343-559 Cupredoxins -  blue copper proteins                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..ee..............eeeeeeeeeeeeeee.....eeeeeeee........eeee...eeeeeeeee.......eeee......hhhhh..............eeeeeeee....eeeeeee...hhhhhh.eeeeeee........eeeeeeeeeee...hhhhhhhhhh........eeee...............eeee....eeeeeeee......eeeee....eeeeee..eeeeeeee..eee....eeeeeee......eeeeeee.hhhhh.........eeeeee.........................................hhh.eeeeeee.......eeee...........hhhhhhhhh....hhhhh.........eeeeeeee.........eeeee....eeeeee..............hhhhhhhhh......ee.eeee....eeeeeee....eeeeeee.hhhhhhhh.eeeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 ------------------------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_---------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fu9 B   1 EPTCNTPSNRACWSDGFDINTDYEVSTPDTGVTQSYVFNLTEVDNWMGPDGVVKEKVMLINGNIMGPNIVANWGDTVEVTVINNLVTNGTSIHWHGIHQKDTNLHDGANGVTECPIPPKGGQRTYRWRARQYGTSWYHSHFSAQYGNGVVGTIQINGPASLPYDIDLGVFPITDYYYRAADDLVHFTQNNAPPFSDNVLINGTAVNPNTGEGQYANVTLTPGKRHRLRILNTSTENHFQVSLVNHTMTVIAADMVPVNAMTVDSLFLAVGQRYDVVIDASRAPDNYWFNVTFGGQAACGGSLNPHPAAIFHYAGAPGGLPTDEGTPPVDHQCLDTLDVRPVVPRSVPVNSFVKRPDNTLPVALDLTGTPLFVWKVNGSDINVDWGKPIIDYILTGNTSYPVSDNIVQVDAVDQWTYWLIENDPEGPFSLPHPMHLHGHDFLVLGRSPDVPAASQQRFVFDPAVDLARLNGDNPPRRDTTMLPAGGWLLLAFRTDNPGAWLFHCHIAWHVSGGLSVDFLERPADLRQRISQEDEDDFNRVCDEWRAYWPTNPYPKIDSGL 559
                                    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       520       530       540       550
   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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FU9)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LAC1_MELAO | Q70KY3)
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:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    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:0043245    extraorganismal space    The environmental space outside of an organism; this may be a host organism in the case of parasitic and symbiotic organisms.

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  LAC1_MELAO | Q70KY3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LAC1_MELAO | Q70KY3: 1gw0 2ih8 2ih9 2q9o 3dkh 3fu7 3fu8 3qpk

(-) Related Entries Specified in the PDB File

2q9o NATIVE RMAL STRUCTURE
3fu7
3fu8