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(-) Description

Title :  CRYSTAL STRUCTURE OF LACCASE FROM CERRENA MAXIMA AT 1.9A RESOLUTION
 
Authors :  A. V. Lyashenko, A. G. Gabdoulkhakov, V. N. Zaitsev, V. S. Lamzin, P. F. L I. Bento, C. Betzel, N. E. Zhukhlistova, Y. N. Zhukova, A. M. Mikhailov
Date :  27 May 06  (Deposition) - 29 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Blue Multi-Copper Enzyme, Laccase From Cerrena Maxima, Purification, Crystals, X-Ray Analyses, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. V. Lyashenko, N. E. Zhukhlistova, A. G. Gabdoulkhakov, V. N. Zaitsev, I. Bento, V. S. Lamzin, C. Betzel, P. F. Lindley, O. V. Koroleva, Y. N. Zhukova, E. V. Stepanova, E. Y. Morgunova, W. Voelter, K. Schirwitz, V. I. Tishkov, G. S. Kachalova, E. A. Cherkashyn, A. M. Mikhailov
Purification, Crystallization And Preliminary X-Ray Study O The Fungal Laccase From Cerrena Maxima
Acta Crystallogr. , Sect. F V. 62 954 2006
PubMed-ID: 17012782  |  Reference-DOI: 10.1107/S1744309106036578

(-) Compounds

Molecule 1 - LACCASE
    Chains: A
    EC Number: 1.10.3.2
    Organism Scientific: TRAMETES MAXIMA
    Organism Taxid: 259368
    Strain: 0275 (MONT)KRAISEL OF THE POLYPORACEAE FAMILY

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NIY2Mod. Amino AcidMETA-NITRO-TYROSINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:23 , ASN A:54 , MET A:57 , ALA A:155 , LEU A:158 , NAG A:501 , HOH A:1029 , HOH A:1035 , HOH A:1102BINDING SITE FOR RESIDUE NAG A 500
02AC2SOFTWAREARG A:22 , HIS A:153 , THR A:154 , ALA A:155 , LEU A:158 , NAG A:500 , MAN A:502 , HOH A:662 , HOH A:670 , HOH A:920 , HOH A:1033 , HOH A:1035BINDING SITE FOR RESIDUE NAG A 501
03AC3SOFTWAREPHE A:20 , NAG A:501 , MAN A:503 , HOH A:978 , HOH A:1033 , HOH A:1075 , HOH A:1114BINDING SITE FOR RESIDUE MAN A 502
04AC4SOFTWAREPRO A:4 , VAL A:5 , PHE A:20 , SER A:21 , MAN A:502 , MAN A:504 , HOH A:821 , HOH A:893 , HOH A:1047 , HOH A:1113BINDING SITE FOR RESIDUE MAN A 503
05AC5SOFTWAREPRO A:4 , ALA A:14 , SER A:21 , ASN A:39 , ASP A:42 , MAN A:503 , HOH A:662 , HOH A:680 , HOH A:860 , HOH A:901 , HOH A:1033BINDING SITE FOR RESIDUE MAN A 504
06AC6SOFTWAREPRO A:160 , GLY A:215 , ASN A:217 , GLN A:252 , GLN A:298 , NAG A:506 , HOH A:709 , HOH A:909 , HOH A:1121BINDING SITE FOR RESIDUE NAG A 505
07AC7SOFTWARELYS A:157 , LEU A:158 , GLY A:159 , NAG A:505 , MAN A:507 , HOH A:984BINDING SITE FOR RESIDUE NAG A 506
08AC8SOFTWARELYS A:157 , NAG A:506 , HOH A:984BINDING SITE FOR RESIDUE MAN A 507
09AC9SOFTWAREASN A:333 , SER A:335 , ASN A:336 , PHE A:338BINDING SITE FOR RESIDUE NAG A 508
10BC1SOFTWAREASN A:327 , SER A:383 , PRO A:385 , ASN A:436 , GLN A:482 , HOH A:839 , HOH A:986 , HOH A:991 , HOH A:1052 , HOH A:1107BINDING SITE FOR RESIDUE NAG A 509
11BC2SOFTWAREHIS A:395 , CYS A:453 , ILE A:455 , HIS A:458BINDING SITE FOR RESIDUE CU A 601
12BC3SOFTWAREHIS A:66 , TRP A:107 , HIS A:109 , HIS A:454 , HOH A:1132BINDING SITE FOR RESIDUE CU A 602
13BC4SOFTWAREHIS A:111 , HIS A:400 , HIS A:452 , HOH A:1132BINDING SITE FOR RESIDUE CU A 603
14BC5SOFTWAREHIS A:64 , HIS A:66 , HIS A:398 , HIS A:400 , HOH A:607BINDING SITE FOR RESIDUE CU A 604

(-) 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 2H5U)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTICOPPER_OXIDASE1PS00079 Multicopper oxidases signature 1.LAC1_TRAMX104-124  1A:104-124

(-) Exons   (0, 0)

(no "Exon" information available for 2H5U)

(-) 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 LAC1_TRAMX | D0VWU3 from UniProtKB/Swiss-Prot  Length:499

    Alignment length: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         
           LAC1_TRAMX     1 AVGPVADNTITDAATSPDGFSRQAVVVNGVTPGPLVAGNIGDRFQLNVIDNLTNHTMLKTTSVHWHGFFQQGTNWADGPAFINQCPISPGHSFLYDFQVPNQAGTFWYHSHLSTQYCDGLRGPFVVYDPNDPHASRYDVDNDDTVITLADWYHTAAKLGPRFPAGADATLINGKGRAPSDTSAELSVIKVTKGKRYRFRLVSLSCDPNFTFSIDGHNLTIIEVDSSNSQPLSVDSIQIFAAQRYSFVLNANQAVDNYWIRANPNFGNVGFNGGINSAILRYDGAPAVEPTTNQTTSVKPLNEVNLHPLVSTPVPGSPSSGGVDKAINMAFNFNGSNFFINGASFVPPSVPVLLQILSGAQTAQDLLPSGSVYVLPSNASIEISFPATAAAPGAPHPFHLHGHTFAVVRSAGSTVYNYSNPIFRDVVSTGTPAAGDNVTIRFLTNNPGPWFLHCHIDFHLEGGFAVVQAEDVPDVKATNPVPQAWSDLCPTYDANAPSDQ 499
               SCOP domains d2h5ua1 A:1-130 automated matches                                                                                                 d2h5ua2 A:131-300 automated matches                                                                                                                                       d2h5ua3 A:301-499 automated matches                                                                                                                                                                     SCOP domains
               CATH domains 2h5uA01 A:1-132 Cupredoxins -  blue copper proteins                                                                                 2h5uA02 A:133-309 Cupredoxins -  blue copper proteins                                                                                                                            2h5uA03 A:310-499 Cupredoxins -  blue copper proteins                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee......eeeeee........eeee...eeeeeeee...hhhhh....eeee......hhhhh.............eeeeeeee.....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........eeeeeee....eeeeeee.hhhhhhh..eeeeee...hhhhhh..hhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h5u A   1 GVGPVADNTITNAATSPDGFSRQAVVVNGVTPGPLVAGNIGDRFQLNVIDNLTNHTMLKTTSVHWHGFFQQGTNWADGPAFINQCPISPGHSFLYDFQVPNQAGTFWYHSHLSTQYCDGLRGPFVVYDPNDPHASRYDVDNDDTTITLADWYHTAAKLGPAFPNGADSTLINGKGRAPSDSSAQLSVVSVTKGKRyRFRLVSLSCDPNFTFSIDGHNNTIIETDSVNSQPLNTDSIQIFAAQRYSFTLNANQAVDNYWIRANPNFGNVGFNGGINSAILRYDGAPAVEPTTNQSTSTQPLNETNLHPLVSTPVPGSPAAGGVDKAINMAFNFNGSNFFINGASFTPPSVPVLLQILSGAQTAQDLLPSGSVyTLPSNASIEISFPATAAAPGAPHPFHLHGHVFAVVRSAGSTVYNYSNPIFRDVVSTGTPAAGDNVTIRFLTNNPGPWFLHCHIDFHLEGGFAVVQAEDVPDVKATNPVPQAWSDLCPTYDANAPSDQ 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         
                                                                                                                                                                                                                             196-NIY                                                                                                                                                                         372-NIY
   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  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H5U)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LAC1_TRAMX | D0VWU3)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        LAC1_TRAMX | D0VWU3: 3div

(-) Related Entries Specified in the PDB File

1kya ACTIVE LACCASE FROM TRAMETES VERSICOLOR COMPLEXED WITH 2,5- XYLIDINE