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(-) Description

Title :  CRYSTAL STRUCTURE OF LACB FROM TRAMETES SP. AH28-2
 
Authors :  H. H. Ge, M. K. Teng, L. W. Niu
Date :  01 Dec 09  (Deposition) - 09 Mar 10  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.44
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Laccase, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. H. Ge, Y. X. Gao, Y. Z. Hong, M. Zhang, Y. Z. Xiao, M. K. Teng, L. W. Niu
Structure Of Native Laccase B From Trametes Sp. Ah28-2
Acta Crystallogr. , Sect. F V. 66 254 2010
PubMed-ID: 20208154  |  Reference-DOI: 10.1107/S1744309110000084

(-) Compounds

Molecule 1 - LACCASE B
    Chains: A, B
    EC Number: 1.10.3.2
    Fragment: UNP RESIDUES 24-525
    Organism Scientific: TRAMETES
    Organism Taxid: 306582
    Strain: AH28-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1CU8Ligand/IonCOPPER (II) ION
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:400 , CYS A:456 , ILE A:458 , HIS A:461BINDING SITE FOR RESIDUE CU A 601
02AC2SOFTWAREHIS A:64 , HIS A:66 , HIS A:403 , HIS A:405BINDING SITE FOR RESIDUE CU A 602
03AC3SOFTWAREHIS A:111 , HIS A:405 , HIS A:455BINDING SITE FOR RESIDUE CU A 603
04AC4SOFTWAREHIS A:66 , TRP A:107 , HIS A:109 , HIS A:457BINDING SITE FOR RESIDUE CU A 604
05AC5SOFTWAREASN A:217 , ASP A:234 , GLN A:252BINDING SITE FOR RESIDUE NAG A 701
06AC6SOFTWAREALA A:23 , ASN A:54 , MET A:57 , NAG A:703BINDING SITE FOR RESIDUE NAG A 702
07AC7SOFTWAREARG A:22 , HIS A:153 , ALA A:155 , LEU A:158 , NAG A:702BINDING SITE FOR RESIDUE NAG A 703
08AC8SOFTWAREASN A:439 , NAG A:705BINDING SITE FOR RESIDUE NAG A 704
09AC9SOFTWAREASN A:327 , HOH A:510 , HOH A:511 , HOH A:519 , NAG A:704BINDING SITE FOR RESIDUE NAG A 705
10BC1SOFTWAREASN A:333 , THR A:335 , ASN A:336 , PHE A:338 , HOH A:516BINDING SITE FOR RESIDUE NAG A 706
11BC2SOFTWAREHIS B:400 , CYS B:456 , ILE B:458 , HIS B:461BINDING SITE FOR RESIDUE CU B 601
12BC3SOFTWAREHIS B:64 , HIS B:403 , HIS B:405BINDING SITE FOR RESIDUE CU B 602
13BC4SOFTWAREHIS B:111 , HIS B:405 , HIS B:455BINDING SITE FOR RESIDUE CU B 603
14BC5SOFTWAREHIS B:66 , TRP B:107 , HIS B:109 , HIS B:457BINDING SITE FOR RESIDUE CU B 604
15BC6SOFTWAREALA B:23 , ASN B:54 , MET B:57 , ALA B:155 , NAG B:702BINDING SITE FOR RESIDUE NAG B 701
16BC7SOFTWAREARG B:22 , HIS B:153 , ALA B:155 , LEU B:158 , HOH B:506 , NAG B:701BINDING SITE FOR RESIDUE NAG B 702
17BC8SOFTWAREASN B:439 , NAG B:704BINDING SITE FOR RESIDUE NAG B 703
18BC9SOFTWAREASN B:327 , HOH B:508 , HOH B:509 , HOH B:510 , NAG B:703BINDING SITE FOR RESIDUE NAG B 704
19CC1SOFTWAREGLY B:215 , HIS B:216 , ASN B:217 , GLN B:252 , ILE B:298BINDING SITE FOR RESIDUE NAG B 705
20CC2SOFTWAREASN B:333 , THR B:335BINDING SITE FOR RESIDUE NAG B 706

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:85 -A:491
2A:117 -A:205
3B:85 -B:491
4B:117 -B:205

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:3 -Pro A:4
2Phe A:31 -Pro A:32
3Leu A:366 -Pro A:367
4Ala A:398 -Pro A:399
5Gly B:3 -Pro B:4
6Phe B:31 -Pro B:32
7Leu B:366 -Pro B:367
8Ala B:398 -Pro B:399

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KW7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KW7)

(-) Exons   (0, 0)

(no "Exon" information available for 3KW7)

(-) Sequences/Alignments

Asymmetric 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:502
 aligned with Q5I7J0_9APHY | Q5I7J0 from UniProtKB/TrEMBL  Length:525

    Alignment length:502
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523  
         Q5I7J0_9APHY    24 AIGPVTDLTISNADVTPDGFTRAAVVANGVFPGPLITGNKGDNFQINVIDNLTNATMLKTTTIHWHGLFQHGTNWADGPAFVNQCPIASGNSFLYDFTVPDQAGTFWYHSHLSTQYCDGLRGPLVVYDPSDPYASMYDVDDDTTVITLSDWYHTAAKLGPAFPPNADSVLINGLGRFAGGNASDLAVITVEQNKRYRFRLVSLSCDPNFTFSIDGHNMTIIEVDGVNHEPLEVDSIQIFASQRYSFVLNATQSVDNYWIRAIPNTGTIDTTGGLNSAILRYSGADIVDPTANATTSVIPLVETDLVPLDSPAAPGDPVVGGVDLAMNLDFSFNGTNFFINNETLIPPTVPVLLQILSGAQSASDLLPTGSVYTLPLNSTIELSFPITTVNGVTNAPGAPHPFHLHGHAFSVVRSAGSSDYNYVNPVRRDTVSTGNPGDNVTIRFTTDNAGPWFLHCHIDFHLEAGFAIVFAEDTPDTASVNPVPTAWSDLCPTYDALDPSDH 525
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3kw7A01 A:1-132 Cupredoxins -  blue copper proteins                                                                                 3kw7A02 A:133-309 Cupredoxins -  blue copper proteins                                                                                                                            3kw7A03 A:310-502 Cupredoxins -  blue copper proteins                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee......eeeeee........eeee...eeeeeeeee..hhhhh....eeee......hhhhhh.............eeeeeee.....eeeeeee...hhhhhh.eeeeeee.............hhh.eeeeeee................eeee..............eeeee....eeeeeeee...............eeeeee..eeeeeeee.eeee....eeeeeee......eeeeeeee............eeeeee...................hhhhh..................eeee..eee....eee..........hhhhhhhh...hhhhh.....eeee....eeeee.................eeee....eeeee.............ee.eee........eeeee....eeeeeee.hhhhhh...eeeeeehhhhhhhhh..hhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kw7 A   1 AIGPVTDLTISNADVTPDGFTRAAVVANGVFPGPLITGNKGDNFQINVIDNLTNATMLKTTTIHWHGLFQHGTNWADGPAFVNQCPIASGNSFLYDFTVPDQAGTFWYHSHLSTQYCDGLRGPLVVYDPSDPYASMYDVDDDTTVITLSDWYHTAAKLGPAFPPNADSVLINGLGRFAGGNASDLAVITVEQNKRYRFRLVSLSCDPNFTFSIDGHNMTIIEVDGVNHEPLEVDSIQIFASQRYSFVLNATQSVDNYWIRAIPNTGTIDTTGGLNSAILRYSGADIVDPTANATTSVIPLVETDLVPLDSPAAPGDPVVGGVDLAMNLDFSFNGTNFFINNETLIPPTVPVLLQILSGAQSASDLLPTGSVYTLPLNSTIELSFPITTVNGVTNAPGAPHPFHLHGHAFSVVRSAGSSDYNYVNPVRRDTVSTGNPGDNVTIRFTTDNAGPWFLHCHIDFHLEAGFAIVFAEDTPDTASVNPVPTAWSDLCPTYDALDPSDH 502
                                    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  


Chain B from PDB  Type:PROTEIN  Length:502
 aligned with Q5I7J0_9APHY | Q5I7J0 from UniProtKB/TrEMBL  Length:525

    Alignment length:502
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523  
         Q5I7J0_9APHY    24 AIGPVTDLTISNADVTPDGFTRAAVVANGVFPGPLITGNKGDNFQINVIDNLTNATMLKTTTIHWHGLFQHGTNWADGPAFVNQCPIASGNSFLYDFTVPDQAGTFWYHSHLSTQYCDGLRGPLVVYDPSDPYASMYDVDDDTTVITLSDWYHTAAKLGPAFPPNADSVLINGLGRFAGGNASDLAVITVEQNKRYRFRLVSLSCDPNFTFSIDGHNMTIIEVDGVNHEPLEVDSIQIFASQRYSFVLNATQSVDNYWIRAIPNTGTIDTTGGLNSAILRYSGADIVDPTANATTSVIPLVETDLVPLDSPAAPGDPVVGGVDLAMNLDFSFNGTNFFINNETLIPPTVPVLLQILSGAQSASDLLPTGSVYTLPLNSTIELSFPITTVNGVTNAPGAPHPFHLHGHAFSVVRSAGSSDYNYVNPVRRDTVSTGNPGDNVTIRFTTDNAGPWFLHCHIDFHLEAGFAIVFAEDTPDTASVNPVPTAWSDLCPTYDALDPSDH 525
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3kw7B01 B:1-132 Cupredoxins -  blue copper proteins                                                                                 3kw7B02 B:133-309 Cupredoxins -  blue copper proteins                                                                                                                            3kw7B03 B:310-502 Cupredoxins -  blue copper proteins                                                                                                                                             CATH domains
           Pfam domains (1) --------Cu-oxidase_3-3kw7B05 B:9-131                                                                                               ----------Cu-oxidase-3kw7B01 B:142-284                                                                                                                   -----------------------------------------------------------Cu-oxidase_2-3kw7B03 B:344-476                                                                                                       -------------------------- Pfam domains (1)
           Pfam domains (2) --------Cu-oxidase_3-3kw7B06 B:9-131                                                                                               ----------Cu-oxidase-3kw7B02 B:142-284                                                                                                                   -----------------------------------------------------------Cu-oxidase_2-3kw7B04 B:344-476                                                                                                       -------------------------- Pfam domains (2)
         Sec.struct. author ....eeeeeeeeeee......eeeeee........eeee...eeeeeeeee..hhhhh....eeee......hhhhh..............eeeeeee.....eeeeeee...hhhhhh.eeeeeee.............hhh.eeeeeee................eeee...............eeee....eeeeeeee...............eeeeee..eeeeeeee.eeee....eeeeeee......eeeeeeee............eeeeee...................hhhhh..................eeee..eee....eee..........hhhhhhhh.............eeee....eeeeeeee..............eeee....eeeee.............ee.eee.....eeeeeeee....eeeeeee.hhhhhh...eeeeeehhhhhhhhh..hhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kw7 B   1 AIGPVTDLTISNADVTPDGFTRAAVVANGVFPGPLITGNKGDNFQINVIDNLTNATMLKTTTIHWHGLFQHGTNWADGPAFVNQCPIASGNSFLYDFTVPDQAGTFWYHSHLSTQYCDGLRGPLVVYDPSDPYASMYDVDDDTTVITLSDWYHTAAKLGPAFPPNADSVLINGLGRFAGGNASDLAVITVEQNKRYRFRLVSLSCDPNFTFSIDGHNMTIIEVDGVNHEPLEVDSIQIFASQRYSFVLNATQSVDNYWIRAIPNTGTIDTTGGLNSAILRYSGADIVDPTANATTSVIPLVETDLVPLDSPAAPGDPVVGGVDLAMNLDFSFNGTNFFINNETLIPPTVPVLLQILSGAQSASDLLPTGSVYTLPLNSTIELSFPITTVNGVTNAPGAPHPFHLHGHAFSVVRSAGSSDYNYVNPVRRDTVSTGNPGDNVTIRFTTDNAGPWFLHCHIDFHLEAGFAIVFAEDTPDTASVNPVPTAWSDLCPTYDALDPSDH 502
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 3KW7)

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5I7J0_9APHY | Q5I7J0)
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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