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(-) Description

Title :  SMALL LACCASE FROM STREPTOMYCES VIRIDOSPORUS T7A; ALTERNATE CRYSTAL FORM COMPLEXED WITH ACETOVANILLONE.
 
Authors :  T. Lukk, S. Majumdar, J. A. Gerlt, S. K. Nair
Date :  05 Aug 11  (Deposition) - 29 Aug 12  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Two-Domain Laccase, Oxidoreductase, Acitovanillone, None, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Majumdar, T. Lukk, J. O. Solbiati, S. Bauer, S. K. Nair, J. E. Cronan, J. A. Gerlt
Roles Of Small Laccases From Streptomyces In Lignin Degradation.
Biochemistry V. 53 4047 2014
PubMed-ID: 24870309  |  Reference-DOI: 10.1021/BI500285T

(-) Compounds

Molecule 1 - SMALL LACCASE, TWO-DOMAIN LACCASE, MULTI-COPPER OXIDASE
    Chains: A, B, C
    EC Number: 1.10.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: COPPER OXIDASE
    Organism Scientific: STREPTOMYCES VIRIDOSPORUS
    Organism Taxid: 67581
    Strain: T7A

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
1CU12Ligand/IonCOPPER (II) ION
2I751Ligand/Ion1-(4-HYDROXY-3-METHOXYPHENYL)ETHANONE
3OXY2Ligand/IonOXYGEN MOLECULE
4PO47Ligand/IonPHOSPHATE ION
5TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE
Biological Unit 1 (4, 11)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2I751Ligand/Ion1-(4-HYDROXY-3-METHOXYPHENYL)ETHANONE
3OXY2Ligand/IonOXYGEN MOLECULE
4PO47Ligand/IonPHOSPHATE ION
5TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE
Biological Unit 2 (4, 22)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2I752Ligand/Ion1-(4-HYDROXY-3-METHOXYPHENYL)ETHANONE
3OXY4Ligand/IonOXYGEN MOLECULE
4PO414Ligand/IonPHOSPHATE ION
5TAM2Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:226 , CYS A:283 , HIS A:288 , MET A:293BINDING SITE FOR RESIDUE CU A 5
02AC2SOFTWAREOXY A:1 , HIS A:231 , HIS A:282 , HIS B:153BINDING SITE FOR RESIDUE CU A 8
03AC3SOFTWAREHIS A:99 , HIS A:151 , HIS C:284 , OXY C:348BINDING SITE FOR RESIDUE CU A 12
04AC4SOFTWARECU A:8 , HIS A:229 , HIS A:231 , HIS A:282 , HIS A:284 , HIS B:97 , HIS B:153 , CU B:347 , HOH B:352BINDING SITE FOR RESIDUE OXY A 1
05AC5SOFTWAREARG A:135 , TRP A:140 , ARG A:141 , ALA A:142 , HOH A:374 , HOH A:420 , GLY C:241 , MET C:242 , LEU C:243BINDING SITE FOR RESIDUE PO4 A 344
06AC6SOFTWAREHOH A:14 , PRO A:70 , HIS A:186 , THR A:187 , ASN A:196 , PHE A:206 , HOH A:354 , HOH A:438BINDING SITE FOR RESIDUE PO4 A 4
07AC7SOFTWAREHIS B:229 , HIS B:231 , HIS C:97BINDING SITE FOR RESIDUE CU B 344
08AC8SOFTWAREHIS B:231 , HIS B:282 , HIS C:153 , HOH C:424BINDING SITE FOR RESIDUE CU B 345
09AC9SOFTWAREHIS B:226 , CYS B:283 , HIS B:288 , MET B:293BINDING SITE FOR RESIDUE CU B 346
10BC1SOFTWAREOXY A:1 , HIS A:284 , HIS B:99 , HIS B:151BINDING SITE FOR RESIDUE CU B 347
11BC2SOFTWAREHIS A:229 , HIS B:97 , VAL B:98 , TYR B:103BINDING SITE FOR RESIDUE CU B 348
12BC3SOFTWAREGLY A:241 , MET A:242 , LEU A:243 , ARG B:135 , TRP B:140 , ARG B:141 , ALA B:142 , HOH B:355 , HOH B:424BINDING SITE FOR RESIDUE PO4 B 349
13BC4SOFTWARETHR B:187 , ASN B:196 , HOH B:439 , HOH B:444BINDING SITE FOR RESIDUE PO4 B 350
14BC5SOFTWAREARG B:52 , LYS B:111 , VAL B:154 , GLY B:156 , THR B:157 , GLU B:158 , HOH B:360 , HOH B:404BINDING SITE FOR RESIDUE PO4 B 351
15BC6SOFTWAREHIS B:284 , HIS C:99 , HIS C:151 , HOH C:424BINDING SITE FOR RESIDUE CU C 344
16BC7SOFTWAREHIS C:226 , CYS C:283 , HIS C:288 , MET C:293BINDING SITE FOR RESIDUE CU C 345
17BC8SOFTWAREHIS A:153 , HIS C:231 , HIS C:282 , OXY C:348BINDING SITE FOR RESIDUE CU C 346
18BC9SOFTWAREHIS A:97 , HIS C:229 , HIS C:231 , OXY C:348BINDING SITE FOR RESIDUE CU C 347
19CC1SOFTWARECU A:12 , HIS A:97 , HIS A:153 , HIS C:229 , HIS C:231 , HIS C:282 , HIS C:284 , CU C:346 , CU C:347BINDING SITE FOR RESIDUE OXY C 348
20CC2SOFTWAREASP C:192 , MET C:193 , THR C:194 , ALA C:200 , TAM C:350 , HOH C:436BINDING SITE FOR RESIDUE I75 C 349
21CC3SOFTWAREGLN C:57 , ARG C:165 , ASN C:191 , ASP C:192 , THR C:194 , ASN C:197 , MET C:291 , I75 C:349 , HOH C:404BINDING SITE FOR RESIDUE TAM C 350
22CC4SOFTWAREPRO C:70 , HIS C:186 , THR C:187 , ASN C:196 , HOH C:360 , HOH C:369BINDING SITE FOR RESIDUE PO4 C 351
23CC5SOFTWAREMET B:242 , LEU B:243 , ARG C:135 , TRP C:140 , ARG C:141 , ALA C:142 , HOH C:386 , HOH C:451BINDING SITE FOR RESIDUE PO4 C 352

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TBC)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ile A:69 -Pro A:70
2Gly A:203 -Pro A:204
3Ile B:69 -Pro B:70
4Gly B:203 -Pro B:204
5Ile C:69 -Pro C:70
6Gly C:203 -Pro C:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TBC)

(-) 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:279
 aligned with J9PBR2_STRVD | J9PBR2 from UniProtKB/TrEMBL  Length:313

    Alignment length:279
                                    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         
         J9PBR2_STRVD     1 MGPAKTAPAGGEVKRIKLYAERLGGGQMGYGLEKGKATIPGPLIELNEGDTLHIEFENTMDVPVSLHVHGLDYEISSDGTKQSRSDVEPGGTRTYTWRTHVPGRRADGTWRAGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDRTHTIVFNDMTINNRPAHTGPDFEATVGDRVEFVMITHGEYYHTFHLHGHRWADNRTGMLTGPDDPSQVIDNKICGPADSFGFQVIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGY 279
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee.hhh.eeee............eeee...eeeeeeee........ee.....hhhhh.............eeeeeee....ee.....ee....eeeeee........hhhhhhh..eeeeeee........eeeeeeee..ee..........eeee...eeeeeeeee....eeeee....ee...............ee.eeee....eeeeeee.......eeeeeee.hhhhhhh..eeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tbc A  31 MGPAKTAPAGGEVKRIKLYAERLGGGQMGYGLEKGKATIPGPLIELNEGDTLHIEFENTMDVPVSLHVHGLDYEISSDGTKQSRSDVEPGGTRTYTWRTHVPGRRADGTWRAGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDRTHTIVFNDMTINNRPAHTGPDFEATVGDRVEFVMITHGEYYHTFHLHGHRWADNRTGMLTGPDDPSQVIDNKICGPADSFGFQVIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGY 309
                                    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         


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with J9PBR2_STRVD | J9PBR2 from UniProtKB/TrEMBL  Length:313

    Alignment length:278
                                    11        21        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        
         J9PBR2_STRVD     2 GPAKTAPAGGEVKRIKLYAERLGGGQMGYGLEKGKATIPGPLIELNEGDTLHIEFENTMDVPVSLHVHGLDYEISSDGTKQSRSDVEPGGTRTYTWRTHVPGRRADGTWRAGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDRTHTIVFNDMTINNRPAHTGPDFEATVGDRVEFVMITHGEYYHTFHLHGHRWADNRTGMLTGPDDPSQVIDNKICGPADSFGFQVIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGY 279
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeeehhheeeee............eeee...eeeeeeee........ee.....hhhhh.............eeeeeee....ee.....ee....eeeeee........hhhhhhhh.eeeeeee........eeeeeeee..ee..........eeee...eeeeeeeee....eeeee....ee...............ee.eeee....eeeeeee.......eeeeeee.hhhhhhh..eeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tbc B  32 GPAKTAPAGGEVKRIKLYAERLGGGQMGYGLEKGKATIPGPLIELNEGDTLHIEFENTMDVPVSLHVHGLDYEISSDGTKQSRSDVEPGGTRTYTWRTHVPGRRADGTWRAGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDRTHTIVFNDMTINNRPAHTGPDFEATVGDRVEFVMITHGEYYHTFHLHGHRWADNRTGMLTGPDDPSQVIDNKICGPADSFGFQVIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGY 309
                                    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        


Chain C from PDB  Type:PROTEIN  Length:277
 aligned with J9PBR2_STRVD | J9PBR2 from UniProtKB/TrEMBL  Length:313

    Alignment length:277
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       
         J9PBR2_STRVD     3 PAKTAPAGGEVKRIKLYAERLGGGQMGYGLEKGKATIPGPLIELNEGDTLHIEFENTMDVPVSLHVHGLDYEISSDGTKQSRSDVEPGGTRTYTWRTHVPGRRADGTWRAGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDRTHTIVFNDMTINNRPAHTGPDFEATVGDRVEFVMITHGEYYHTFHLHGHRWADNRTGMLTGPDDPSQVIDNKICGPADSFGFQVIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGY 279
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee.hhh.eeee............eeee...eeeeeeee........ee.....hhhhh.............eeeeee.....ee.....ee....eeeeee........hhhhhhhh.eeeeeee........eeeeeeee..ee.........eeeee...eeeeeeeee....eeeee....ee...............ee.eeee....eeeeeee.......eeeeeee.hhhhhhhh.eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tbc C  33 PAKTAPAGGEVKRIKLYAERLGGGQMGYGLEKGKATIPGPLIELNEGDTLHIEFENTMDVPVSLHVHGLDYEISSDGTKQSRSDVEPGGTRTYTWRTHVPGRRADGTWRAGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDRTHTIVFNDMTINNRPAHTGPDFEATVGDRVEFVMITHGEYYHTFHLHGHRWADNRTGMLTGPDDPSQVIDNKICGPADSFGFQVIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGY 309
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (J9PBR2_STRVD | J9PBR2)
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

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

UniProtKB/TrEMBL
        J9PBR2_STRVD | J9PBR2: 3tas 3tbb

(-) Related Entries Specified in the PDB File

3tas SAME PROTEIN, ALTERNATE CRYSTAL FORM COMPLEXED WITH CU AND ZN
3tbb SAME PROTEIN, UNLIGANDED STRUCTURE IN THE SAME CRYSTAL FORM