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(-) Description

Title :  X-RAY INDUCED REDUCTION OF LACCASE FROM THERMUS THERMOPHILUS HB27 (25.0-37.5 PERCENT DOSE)
 
Authors :  H. Serrano-Posada, E. Rudino-Pinera
Date :  22 Feb 11  (Deposition) - 29 Feb 12  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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 Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET32A
    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 Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1CU3Ligand/IonCOPPER (II) ION
2MPD10Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD6Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4OH1Ligand/IonHYDROXIDE ION
Biological Unit 1 (2, 32)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2MPD20Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD12Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4OH-1Ligand/IonHYDROXIDE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:97 , TRP A:133 , HIS A:135 , HIS A:446 , OH A:1481BINDING SITE FOR RESIDUE CU A1462
02AC2SOFTWAREHIS A:393 , CYS A:445 , HIS A:450 , MET A:455BINDING SITE FOR RESIDUE CU A1463
03AC3SOFTWAREHIS A:95 , HIS A:137 , HIS A:396 , HIS A:398 , HIS A:444 , OH A:1481BINDING SITE FOR RESIDUE CU A1464
04AC4SOFTWAREASP A:248 , LEU A:263 , GLU A:267 , ARG A:268 , TYR A:414 , LYS A:418 , MPD A:1470BINDING SITE FOR RESIDUE MPD A1465
05AC5SOFTWAREGLN A:56 , ARG A:436 , HOH A:2501 , HOH A:2502BINDING SITE FOR RESIDUE MRD A1466
06AC6SOFTWAREMET A:295 , MET A:355BINDING SITE FOR RESIDUE MRD A1467
07AC7SOFTWARELYS A:104 , THR A:212 , ARG A:280 , HOH A:2499 , HOH A:2503BINDING SITE FOR RESIDUE MRD A1468
08AC8SOFTWAREGLY A:140 , ARG A:453BINDING SITE FOR RESIDUE MPD A1469
09AC9SOFTWAREGLU A:260 , LEU A:261 , MPD A:1465 , HOH A:2314BINDING SITE FOR RESIDUE MPD A1470
10BC1SOFTWAREGLU A:127 , LEU A:128 , SER A:158 , SER A:334 , HOH A:2504BINDING SITE FOR RESIDUE MPD A1471
11BC2SOFTWAREGLU A:257 , SER A:259 , MRD A:1479 , HOH A:2305 , HOH A:2322BINDING SITE FOR RESIDUE MPD A1472
12BC3SOFTWAREPRO A:342 , VAL A:343 , VAL A:344 , THR A:345BINDING SITE FOR RESIDUE MPD A1473
13BC4SOFTWAREPRO A:28 , GLU A:29 , PRO A:30 , ASN A:206 , MPD A:1478 , HOH A:2056 , HOH A:2087 , HOH A:2089BINDING SITE FOR RESIDUE MRD A1474
14BC5SOFTWAREPRO A:25 , SER A:26 , GLN A:216 , ASN A:362 , GLN A:364 , HOH A:2005 , HOH A:2269 , HOH A:2505BINDING SITE FOR RESIDUE MPD A1475
15BC6SOFTWARELYS A:31 , GLY A:64 , HOH A:2086BINDING SITE FOR RESIDUE MPD A1476
16BC7SOFTWAREPRO A:191 , ALA A:356 , ARG A:453BINDING SITE FOR RESIDUE MPD A1477
17BC8SOFTWARESER A:26 , GLN A:376 , ALA A:377 , GLN A:378 , THR A:379 , MRD A:1474 , HOH A:2004BINDING SITE FOR RESIDUE MPD A1478
18BC9SOFTWAREARG A:276 , MPD A:1472 , HOH A:2371 , HOH A:2506 , HOH A:2507BINDING SITE FOR RESIDUE MRD A1479
19CC1SOFTWAREPRO A:144 , PRO A:188 , HIS A:189 , TRP A:194 , HOH A:2201 , HOH A:2244 , HOH A:2508BINDING SITE FOR RESIDUE MRD A1480
20CC2SOFTWAREHIS A:95 , HIS A:135 , HIS A:137 , HIS A:444 , HIS A:446 , CU A:1462 , CU A:1464 , HOH A:2509BINDING SITE FOR RESIDUE OH A1481

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YAH)

(-) 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: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..ee..eee....eeeeeeee......eeeee....eeeeee..eeeeeeeee..eee....eeeeeee....eeeeeeee......eeee......eeee......eeeeeeee.......................eeeeeeeeee....eeee...........eeee...eeeeeeee.....eeeee....eeeeee..ee.....ee.eeee....eeeeeee....eeeeeee.hhhhhhh..eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yah 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 2YAH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric 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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  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 2xvb 2yae 2yaf 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
2xvb 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.
2yae X-RAY INDUCED REDUCTION OF LACCASE FROM THERMUS THERMOPHILUS HB27(0.0-12.5 PERCENT DOSE)
2yaf X-RAY INDUCED REDUCTION OF LACCASE FROM THERMUS THERMOPHILUS HB27 (12.5-25.0 PERCENT DOSE)
2yam X-RAY INDUCED REDUCTION OF LACCASE FROM THERMUS THERMOPHILUS HB27 (37.5-50.0 PERCENT DOSE)
2yao X-RAY INDUCED REDUCTION OF LACCASE FROM THERMUS THERMOPHILUS HB27 (50.0-62.5 PERCENT DOSE)
2yap X-RAY INDUCED REDUCTION OF LACCASE FROM THERMUS THERMOPHILUS HB27 (62.5-75.0 PERCENT DOSE)
2yaq X-RAY INDUCED REDUCTION OF LACCASE FROM THERMUS THERMOPHILUS HB27 (75.0-87.5 PERCENT DOSE)
2yar X-RAY INDUCED REDUCTION OF LACCASE FROM THERMUS THERMOPHILUS HB27 (87.5-100.0 PERCENT DOSE)