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(-) Description

Title :  CRYSTAL STRUCTURE OF LACCASE FROM THERMUS THERMOPHILUS HB27 COMPLEXED WITH HG, CRYSTAL OF THE APOENZYME SOAKED FOR 5 MIN. IN 5 MM HGCL2 AT 278 K.
 
Authors :  H. Serrano-Posada, B. Valderrama, E. Rudino-Pinera
Date :  25 Oct 10  (Deposition) - 26 Oct 11  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Multicopper Oxidases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Serrano-Posada, S. Centeno-Leija, S. P. Rojas-Trejo, C. Rodriguez-Almazan, V. Stojanoff, E. Rudino-Pinera
X-Ray-Induced Catalytic Active-Site Reduction Of A Multicopper Oxidase: Structural Insights Into The Proton- Relay Mechanism And O2-Reduction States.
Acta Crystallogr. , Sect. D V. 71 2396 2015
PubMed-ID: 26627648  |  Reference-DOI: 10.1107/S1399004715018714

(-) Compounds

Molecule 1 - LACCASE
    Chains: A
    EC Number: 1.10.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: MATURE FORM, RESIDUES 24-462
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric/Biological Unit (3, 22)
No.NameCountTypeFull Name
1HG5Ligand/IonMERCURY (II) ION
2MPD11Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD6Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:393 , CYS A:445 , HIS A:450 , MET A:455BINDING SITE FOR RESIDUE HG A1463
02AC2SOFTWAREHIS A:97 , TRP A:133 , HIS A:135 , HIS A:446 , HOH A:2434BINDING SITE FOR RESIDUE HG A1464
03AC3SOFTWAREHIS A:95 , HIS A:97 , HIS A:396 , HIS A:398BINDING SITE FOR RESIDUE HG A1465
04AC4SOFTWAREHIS A:137 , HIS A:398 , HIS A:444 , HOH A:2156 , HOH A:2434BINDING SITE FOR RESIDUE HG A1466
05AC5SOFTWAREMET A:296 , MET A:301 , HIS A:303 , MET A:305BINDING SITE FOR RESIDUE HG A1467
06AC6SOFTWAREALA A:247 , ASP A:248 , LEU A:263 , GLU A:267 , ARG A:268 , TYR A:414 , LYS A:418 , MPD A:1479BINDING SITE FOR RESIDUE MPD A1468
07AC7SOFTWAREARG A:280 , TYR A:317 , HOH A:2440 , HOH A:2442 , HOH A:2443BINDING SITE FOR RESIDUE MPD A1469
08AC8SOFTWAREGLN A:56 , LEU A:339 , HOH A:2055 , HOH A:2444BINDING SITE FOR RESIDUE MRD A1470
09AC9SOFTWAREPRO A:342 , VAL A:343 , VAL A:344 , THR A:345 , HOH A:2338BINDING SITE FOR RESIDUE MRD A1471
10BC1SOFTWAREARG A:75 , PRO A:76 , GLU A:157 , SER A:158 , SER A:159 , HOH A:2173 , HOH A:2445BINDING SITE FOR RESIDUE MPD A1472
11BC2SOFTWAREGLY A:140 , TRP A:194 , ARG A:453 , MPD A:1474 , MPD A:1482BINDING SITE FOR RESIDUE MPD A1473
12BC3SOFTWAREPRO A:144 , PRO A:188 , HIS A:189 , TRP A:194 , MPD A:1473 , HOH A:2160 , HOH A:2198 , HOH A:2446BINDING SITE FOR RESIDUE MPD A1474
13BC4SOFTWAREGLY A:64 , PRO A:70 , HOH A:2068 , HOH A:2448BINDING SITE FOR RESIDUE MPD A1475
14BC5SOFTWAREPRO A:28 , GLU A:29 , PHE A:67 , ASN A:206 , HOH A:2047 , HOH A:2070 , HOH A:2072 , HOH A:2449BINDING SITE FOR RESIDUE MRD A1476
15BC6SOFTWAREPRO A:25 , SER A:26 , GLN A:216 , ASN A:362 , GLN A:364 , HOH A:2004 , HOH A:2006 , HOH A:2450BINDING SITE FOR RESIDUE MPD A1477
16BC7SOFTWAREASP A:289 , GLY A:291 , ASP A:390 , MET A:391 , ASP A:392 , LYS A:424 , ALA A:425 , HOH A:2390 , HOH A:2414BINDING SITE FOR RESIDUE MRD A1478
17BC8SOFTWARELEU A:256 , GLU A:260 , LEU A:261 , MPD A:1468 , HOH A:2452BINDING SITE FOR RESIDUE MPD A1479
18BC9SOFTWAREGLU A:127 , LEU A:128 , SER A:158 , SER A:159 , SER A:334 , HOH A:2453BINDING SITE FOR RESIDUE MPD A1480
19CC1SOFTWAREPRO A:241 , GLU A:257 , MRD A:1483 , HOH A:2262 , HOH A:2454BINDING SITE FOR RESIDUE MPD A1481
20CC2SOFTWAREPRO A:191 , MPD A:1473BINDING SITE FOR RESIDUE MPD A1482
21CC3SOFTWAREHIS A:240 , PRO A:241 , SER A:259 , ARG A:276 , MPD A:1481 , HOH A:2242 , HOH A:2264 , HOH A:2455BINDING SITE FOR RESIDUE MRD A1483
22CC4SOFTWAREMET A:192 , MET A:195 , MET A:354 , MET A:355BINDING SITE FOR RESIDUE MRD A1484

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XVB)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:67 -Pro A:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XVB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XVB)

(-) Exons   (0, 0)

(no "Exon" information available for 2XVB)

(-) 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:439
 aligned with Q72HW2_THET2 | Q72HW2 from UniProtKB/TrEMBL  Length:462

    Alignment length:439
                                    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         
         Q72HW2_THET2    24 GPSFPEPKVVRSQGGLLSLKLSATPTPLALAGQRATLLTYGGSFPGPTLRVRPRDTVRLTLENRLPEPTNLHWHGLPISPKVDDPFLEIPPGESWTYEFTVPKELAGTFWYHPHLHGRVAPQLFAGLLGALVVESSLDAIPELREAEEHLLVLKDLALQGGRPAPHTPMDWMNGKEGDLVLVNGALRPTLVAQKATLRLRLLNASNARYYRLALQDHPLYLIAADGGFLEEPLEVSELLLAPGERAEVLVRLRKEGRFLLQALPYDRGAMGMMDMGGMAHAMPQGPSRPETLLYLIAPKNPKPLPLPKALSPFPTLPAPVVTRRLVLTEDMMAARFFINGQVFDHRRVDLKGQAQTVEVWEVENQGDMDHPFHLHVHPFQVLSVGGRPFPYRAWKDVVNLKAGEVARLLVPLREKGRTVFHCHIVEHEDRGMMGVLEVG 462
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee....eeeeeeeeeeeeeee..eeeeeeee.......eeee....eeeeeeee........eee...................eeeeeee......eeeeee.....hhhhhhhh...eeeee.hhhhhhhhhhh.eeeeeeeeee.ee..ee...hhhhhhhh....eeee......eee....eeeeeeee......eeeee....eeeeee..eeeeeeeee..eee....eeeeeee....eeeeeeee......eee........eee......eeeeeeee.......................eeeeeeeeee....eeee...........eee....eeeeeeee.....eeeee....eeeeee..ee.....ee.eeee....eeeeeee....eeeeeee.hhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xvb A  24 GPSFPEPKVVRSQGGLLSLKLSATPTPLAIAGQRATLLTYGGSFPGPTLRVRPRDTVRLTLENRLPEPTNLHWHGLPISPKVDDPFLEIPPGESWTYEFTVPKELAGTFWYHPHLHGRVAPQLFAGLLGALVVESSLDAIPELREAEEHLLVLKDLALQGGRPAPHTPMDWMNGKEGDLVLVNGALRPTLVAQKATLRLRLLNASNARYYRLALQDHPLYLIAADGGFLEEPLEVSELLLAPGERAEVLVRLRKEGRFLLQALPYDRGAMGMMDMGGMAHAMPQGPSRPETLLYLIAPKNPKPLPLPKALSPFPTLPAPVVTRRLVLTEDMMAARFFINGQVFDHRRVDLKGQAQTVEVWEVENQGDMDHPFHLHVHPFQVLSVGGRPFPYRAWKDVVNLKAGEVARLLVPLREKGRTVFHCHIVEHEDRGMMGVLEVG 462
                                    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
   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 2XVB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XVB)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q72HW2_THET2 | Q72HW2)
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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  2xvb
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  1.10.3.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q72HW2_THET2 | Q72HW2: 5jrr 5jx9 5k0d 5k15 5k3k 5k5k 5k7a 5k84
UniProtKB/TrEMBL
        Q72HW2_THET2 | Q72HW2: 2xu9 2xuw 2yae 2yaf 2yah 2yam 2yao 2yap 2yaq 2yar 4ai7 5afa

(-) Related Entries Specified in the PDB File

2xu9 CRYSTAL STRUCTURE OF LACCASE FROM THERMUS THERMOPHILUS HB27
2xuw CRYSTAL STRUCTURE OF APOLACCASE FROM THERMUS THERMOPHILUS HB27