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(-) Description

Title :  MUTATIONS IN THE NEIGHBOURHOOD OF COTA-LACCASE TRINUCLEAR SITE: D116A MUTANT
 
Authors :  C. S. Silva, P. F. Lindley, I. Bento
Date :  31 Oct 11  (Deposition) - 25 Jan 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Multi-Copper Oxidase, Oxidoreductase Activity, Trinuclear Cluster, Dioxygen Reduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Silva, J. M. Damas, Z. Chen, V. Brissos, L. O. Martins, C. M. Soares P. F. Lindley, I. Bento
The Role Of Asp116 In The Reductive Cleavage Of Dioxygen To Water In Cota Laccase: Assistance During The Proton Transfer Mechanism
Acta Crystallogr. , Sect. D V. 68 186 2012
PubMed-ID: 22281748  |  Reference-DOI: 10.1107/S0907444911054503

(-) Compounds

Molecule 1 - SPORE COAT PROTEIN A
    Chains: A
    EC Number: 1.10.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION
2EDO11Ligand/Ion1,2-ETHANEDIOL
3PER1Ligand/IonPEROXIDE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:419 , CYS A:492 , HIS A:497 , MET A:502BINDING SITE FOR RESIDUE CU A1512
02AC2SOFTWAREHIS A:107 , HIS A:153 , HIS A:493 , PER A:1527BINDING SITE FOR RESIDUE CU A1513
03AC3SOFTWAREHIS A:155 , HIS A:424 , HIS A:491 , CU A:1515 , PER A:1527BINDING SITE FOR RESIDUE CU A1514
04AC4SOFTWAREHIS A:105 , HIS A:107 , HIS A:422 , HIS A:424 , CU A:1514 , PER A:1527 , HOH A:2137BINDING SITE FOR RESIDUE CU A1515
05AC5SOFTWAREPHE A:292 , SER A:293 , TYR A:300 , PRO A:457 , HOH A:2310BINDING SITE FOR RESIDUE EDO A1516
06AC6SOFTWARELEU A:184 , SER A:186 , GLU A:348 , HOH A:2219 , HOH A:2267BINDING SITE FOR RESIDUE EDO A1517
07AC7SOFTWAREARG A:136 , GLU A:137 , VAL A:138 , PRO A:247 , HOH A:2173 , HOH A:2266BINDING SITE FOR RESIDUE EDO A1518
08AC8SOFTWAREALA A:317 , PRO A:328 , ALA A:332 , ASN A:333 , HOH A:2289 , HOH A:2447BINDING SITE FOR RESIDUE EDO A1519
09AC9SOFTWAREGLU A:364 , ARG A:429 , TRP A:463 , ALA A:478 , THR A:480BINDING SITE FOR RESIDUE EDO A1520
10BC1SOFTWAREASP A:113 , TYR A:118 , TYR A:133 , LYS A:135 , ARG A:487 , HOH A:2147BINDING SITE FOR RESIDUE EDO A1521
11BC2SOFTWAREPRO A:284 , ARG A:285 , VAL A:287 , TYR A:358 , PRO A:458 , LYS A:461BINDING SITE FOR RESIDUE EDO A1522
12BC3SOFTWAREPHE A:81 , PRO A:83 , LEU A:206 , PHE A:207 , TYR A:208 , HOH A:2117 , HOH A:2239 , HOH A:2246BINDING SITE FOR RESIDUE EDO A1523
13BC4SOFTWAREGLU A:188 , GLU A:244 , TYR A:250 , HOH A:2224BINDING SITE FOR RESIDUE EDO A1524
14BC5SOFTWARELYS A:25 , TYR A:69 , THR A:307 , ALA A:308 , TYR A:309 , GLU A:310BINDING SITE FOR RESIDUE EDO A1525
15BC6SOFTWAREASN A:75 , LEU A:76 , LYS A:125 , GLN A:367 , LYS A:402BINDING SITE FOR RESIDUE EDO A1526
16BC7SOFTWAREHIS A:105 , HIS A:107 , HIS A:153 , HIS A:155 , HIS A:422 , HIS A:424 , HIS A:491 , HIS A:493 , CU A:1513 , CU A:1514 , CU A:1515 , HOH A:2194BINDING SITE FOR RESIDUE PER A1527

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:229 -A:322

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe A:55 -Pro A:56
2Pro A:217 -Ser A:218
3Asn A:221 -Pro A:222
4Gly A:482 -Pro A:483
5Tyr A:500 -Asp A:501

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A66)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A66)

(-) Exons   (0, 0)

(no "Exon" information available for 4A66)

(-) 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:501
 aligned with COTA_BACSU | P07788 from UniProtKB/Swiss-Prot  Length:513

    Alignment length:510
                                    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       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511
           COTA_BACSU     2 TLEKFVDALPIPDTLKPVQQSKEKTYYEVTMEECTHQLHRDLPPTRLWGYNGLFPGPTIEVKRNENVYVKWMNNLPSTHFLPIDHTIHHSDSQHEEPEVKTVVHLHGGVTPDDSDGYPEAWFSKDFEQTGPYFKREVYHYPNQQRGAILWYHDHAMALTRLNVYAGLVGAYIIHDPKEKRLKLPSDEYDVPLLITDRTINEDGSLFYPSAPENPSPSLPNPSIVPAFCGETILVNGKVWPYLEVEPRKYRFRVINASNTRTYNLSLDNGGDFIQIGSDGGLLPRSVKLNSFSLAPAERYDIIIDFTAYEGESIILANSAGCGGDVNPETDANIMQFRVTKPLAQKDESRKPKYLASYPSVQHERIQNIRTLKLAGTQDEYGRPVLLLNNKRWHDPVTETPKVGTTEIWSIINPTRGTHPIHLHLVSFRVLDRRPFDIARYQESGELSYTGPAVPPPPSEKGWKDTIQAHAGEVLRIAATFGPYSGRYVWHCHILEHEDYDMMRPMDITDP 511
               SCOP domains d4a66a1 A:2-182 automated matches                                                                                                                                                    d4a66a2 A:183-356 automated matches                                                                                                                                           d4a    66a3 A:357-511 automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................ee....eeeeeeeeeeee........eeeeee........eeee....eeeeeee..........hhhhh.-----........eeee....hhhhh.......hhhhh.........eeee......eeeeeee....hhhhhhhhh.eeeeeeehhhhhhhh..hhh.eeeeeeeeeee.....ee........................eeee..ee..eee....eeeeeeee......eeeee.....eeeeee..eeeeeeeee.eeee....eeeeeee.hhhh..eeeeee..............eeeeee.....................----..eeeeeeeeeeeee.....eeeee.................eeeeeeee.....eeeee.....eeeeeee.hhhhhhhhh...........hhhhh....eeee...eeeeeeee.....eeeeeee.hhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4a66 A   2 TLEKFVDALPIPDTLKPVQQSKEKTYYEVTMEECTHQLHRDLPPTRLWGYNGLFPGPTIEVKRNENVYVKWMNNLPSTHFLPIDHTIHH-----EEPEVKTVVHLHGGVTPDDSAGYPEAWFSKDFEQTGPYFKREVYHYPNQQRGAILWYHDHAMALTRLNVYAGLVGAYIIHDPKEKRLKLPSDEYDVPLLITDRTINEDGSLFYPSAPENPSPSLPNPSIVPAFCGETILVNGKVWPYLEVEPRKYRFRVINASNTRTYNLSLDNGGDFIQIGSDGGLLPRSVKLNSFSLAPAERYDIIIDFTAYEGESIILANSAGCGGDVNPETDANIMQFRVTKPLAQKDESRKPKYLASYP----ERIQNIRTLKLAGTQDEYGRPVLLLNNKRWHDPVTETPKVGTTEIWSIINPTRGTHPIHLHLVSFRVLDRRPFDIARYQESGELSYTGPAVPPPPSEKGWKDTIQAHAGEVLRIAATFGPYSGRYVWHCHILEHEDYDMMRPMDITDP 511
                                    11        21        31        41        51        61        71        81        |-    |  101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       | -  |    371       381       391       401       411       421       431       441       451       461       471       481       491       501       511
                                                                                                                   90    96                                                                                                                                                                                                                                                                    359  364
   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  (0, 0)

(no "CATH Domain" information available for 4A66)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A66)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (COTA_BACSU | P07788)
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: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.
    GO:0016722    oxidoreductase activity, oxidizing metal ions    Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
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.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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  4a66
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  COTA_BACSU | P07788
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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
        COTA_BACSU | P07788: 1gsk 1of0 1w6l 1w6w 1w8e 2bhf 2wsd 2x87 2x88 3zdw 4a67 4a68 4ako 4akp 4akq 4q89 4q8b 4yvn 4yvu

(-) Related Entries Specified in the PDB File

1gsk CRYSTAL STRUCTURE OF COTA, AN ENDOSPORE COAT PROTEIN FROM BACILLUS SUBTILIS
1of0 CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER 1H SOAKING WITH ABTS
1uvw BACILLUS SUBTILIS COTA LACCASE ADDUCT WITH ABTS
1w6l 3D STRUCTURE OF COTA INCUBATED WITH CUCL2
1w6w 3D STRUCTURE OF COTA INCUBATED WITH SODIUM AZIDE
1w8e 3D STRUCTURE OF COTA INCUBATED WITH HYDROGEN PEROXIDE
2bhf 3D STRUCTURE OF THE REDUCED FORM OF COTA
2x87 CRYSTAL STRUCTURE OF THE RECONSTITUTED COTA
2x88 CRYSTAL STRUCTURE OF HOLOCOTA
4a67 MUTATIONS IN THE NEIGHBOURHOOD OF COTA-LACCASE TRINUCLEAR SITE: D116E MUTANT
4a68 MUTATIONS IN THE NEIGHBOURHOOD OF COTA-LACCASE TRINUCLEAR SITE: D116N MUTANT