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(-) Description

Title :  PROXIMAL MUTATIONS AT THE TYPE 1 CU SITE OF COTA-LACCASE: I494A MUTANT
 
Authors :  C. S. Silva, P. Durao, Z. Chen, C. M. Soares, M. M. Pereira, S. Todorovic, P. Hildebrandt, L. O. Martins, P. F. Lindley, I. Bento
Date :  04 Sep 09  (Deposition) - 29 Sep 10  (Release) - 29 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Multi-Copper Oxidase, Sporulation, Cota- Laccase, T1 Copper Centre (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Durao, Z. Chen, C. S. Silva, C. M. Soares, M. M. Pereira, S. Todorovic P. Hildebrandt, I. Bento, P. F. Lindley, L. O. Martins
Proximal Mutations At The Type 1 Copper Site Of Cota Laccase: Spectroscopic, Redox, Kinetic And Structural Characterization Of I494A And L386A Mutants.
Biochem. J. V. 412 339 2008
PubMed-ID: 18307408  |  Reference-DOI: 10.1042/BJ20080166

(-) 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
    Other Details: ETHYLENE GLYCOL (EDO) AS SOLVENT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1CSX1Mod. Amino AcidS-OXY CYSTEINE
2CU4Ligand/IonCOPPER (II) ION
3EDO12Ligand/Ion1,2-ETHANEDIOL
4OXY1Ligand/IonOXYGEN MOLECULE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:419 , CYS A:492 , HIS A:497 , MET A:502 , HOH A:2519BINDING SITE FOR RESIDUE CU A 601
02AC2SOFTWAREHIS A:107 , HIS A:153 , HIS A:493 , OXY A:605BINDING SITE FOR RESIDUE CU A 602
03AC3SOFTWAREHIS A:155 , HIS A:424 , HIS A:491 , CU A:604 , OXY A:605BINDING SITE FOR RESIDUE CU A 603
04AC4SOFTWAREHIS A:105 , HIS A:107 , HIS A:422 , HIS A:424 , CU A:603 , OXY A:605 , HOH A:2177BINDING SITE FOR RESIDUE CU A 604
05AC5SOFTWAREHIS 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:602 , CU A:603 , CU A:604BINDING SITE FOR RESIDUE OXY A 605
06AC6SOFTWAREASP A:113 , TYR A:118 , TYR A:133 , LYS A:135 , HOH A:2593BINDING SITE FOR RESIDUE EDO A 701
07AC7SOFTWARELYS A:25 , TYR A:69 , VAL A:138 , THR A:307 , ALA A:308 , TYR A:309 , GLU A:310 , HOH A:2594BINDING SITE FOR RESIDUE EDO A 702
08AC8SOFTWAREASN A:74 , LEU A:76 , PRO A:77 , VAL A:100 , SER A:124 , LYS A:125 , HOH A:2595BINDING SITE FOR RESIDUE EDO A 703
09AC9SOFTWAREGLU A:188 , GLU A:244 , TYR A:250 , HOH A:2596BINDING SITE FOR RESIDUE EDO A 704
10BC1SOFTWAREARG A:136 , GLU A:137 , VAL A:138 , PRO A:247 , HOH A:2597 , HOH A:2598BINDING SITE FOR RESIDUE EDO A 705
11BC2SOFTWAREASP A:268 , ALA A:317 , PRO A:328 , ALA A:332 , ASN A:333 , HOH A:2599 , HOH A:2600BINDING SITE FOR RESIDUE EDO A 706
12BC3SOFTWARELYS A:183 , LEU A:184 , SER A:186 , GLU A:348 , SER A:349 , HOH A:2601BINDING SITE FOR RESIDUE EDO A 707
13BC4SOFTWAREGLU A:61 , ILE A:173 , HIS A:175 , ASP A:190 , PRO A:192 , HOH A:2106 , HOH A:2298 , HOH A:2602 , HOH A:2603BINDING SITE FOR RESIDUE EDO A 708
14BC5SOFTWAREASN A:269 , GLY A:271 , ASP A:272 , ASP A:305 , TYR A:309 , HOH A:2367BINDING SITE FOR RESIDUE EDO A 709
15BC6SOFTWAREVAL A:426 , SER A:427 , THR A:480 , GLY A:482 , HOH A:2253 , HOH A:2573 , HOH A:2605 , HOH A:2606 , HOH A:2607BINDING SITE FOR RESIDUE EDO A 710
16BC7SOFTWARETHR A:130 , GLY A:131 , PHE A:134 , HOH A:2608 , HOH A:2609BINDING SITE FOR RESIDUE EDO A 711
17BC8SOFTWARESER A:186 , TYR A:189 , ARG A:248 , LYS A:346 , GLU A:348 , HOH A:2601BINDING SITE FOR RESIDUE EDO A 712

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WSD)

(-) 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:506
 aligned with COTA_BACSU | P07788 from UniProtKB/Swiss-Prot  Length:513

    Alignment length:511
                                    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 TLEKFVDALPIPDTLKPVQQSKEKTYYEVTMEECTHQLHRDLPPTRLWGYNGLFPGPTIEVKRNENVYVKWMNNLPSTHFLPIDHTIHHSDSQHEEPEVKTVVHLHGGVTPDDSDGYPEAWFSKDFEQTGPYFKREVYHYPNQQRGAILWYHDHAMALTRLNVYAGLVGAYIIHDPKEKRLKLPSDEYDVPLLITDRTINEDGSLFYPSAPENPSPSLPNPSIVPAFCGETILVNGKVWPYLEVEPRKYRFRVINASNTRTYNLSLDNGGDFIQIGSDGGLLPRSVKLNSFSLAPAERYDIIIDFTAYEGESIILANSAGCGGDVNPETDANIMQFRVTKPLAQKDESRKPKYLASYPSVQHERIQNIRTLKLAGTQDEYGRPVLLLNNKRWHDPVTETPKVGTTEIWSIINPTRGTHPIHLHLVSFRVLDRRPFDIARYQESGELSYTGPAVPPPPSEKGWKDTIQAHAGEVLRIAATFGPYSGRYVWHCHILEHEDYDMMRPMDITDPH 512
               SCOP domains d2wsda1 A:2-182 automated matches                                                                                                                                                    d2wsda2 A:183-356 automated matches                                                                                                                                           d2wsda3 A:357-512 automated matches                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cu-oxidase-2wsdA01 A:175-340                                                                                                                                          -----------------Cu-oxidase_2-2wsdA02 A:358-512                                                                                                                              Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------Cu-oxidase_3-2wsdA03 A:96-179                                                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------Cu-oxidase_3-2wsdA04 A:96-179                                                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ..................ee....eeeeeeeeeeee........eeeeee........eeee....eeeeeee................-----........eeee....hhhhh.......hhhhh.........eeee......eeeeeee....hhhhhhhhh.eeeeeeehhhhhhhh..hhh.eeeeeeeeeee.....ee........................eeee..ee..eee....eeeeeeee......eeeee.....eeeeee..eeeeeeeee.eeee....eeeeeee.hhhh..eeeeee..............eeeeee...................hhhhh...eeeeeeeeeeeee.....eeeee.................eeeeeeee.....eeeee.....eeeeeee.hhhhhhhhh...........hhhhh....eeee...eeeeeeee.....eeeeeee.hhhhhh...eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsd A   2 TLEKFVDALPIPDTLKPVQQSKEKTYYEVTMEEcTHQLHRDLPPTRLWGYNGLFPGPTIEVKRNENVYVKWMNNLPSTHFLPIDHTIHH-----EEPEVKTVVHLHGGVTPDDSDGYPEAWFSKDFEQTGPYFKREVYHYPNQQRGAILWYHDHAMALTRLNVYAGLVGAYIIHDPKEKRLKLPSDEYDVPLLITDRTINEDGSLFYPSAPENPSPSLPNPSIVPAFCGETILVNGKVWPYLEVEPRKYRFRVINASNTRTYNLSLDNGGDFIQIGSDGGLLPRSVKLNSFSLAPAERYDIIIDFTAYEGESIILANSAGCGGDVNPETDANIMQFRVTKPLAQKDESRKPKYLASYPSVQHERIQNIRTLKLAGTQDEYGRPVLLLNNKRWHDPVTETPKVGTTEIWSIINPTRGTHPIHLHLVSFRVLDRRPFDIARYQESGELSYTGPAVPPPPSEKGWKDTIQAHAGEVLRIAATFGPYSGRYVWHCHALEHEDYDMMRPMDITDPH 512
                                    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       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511 
                                                            35-CSX                                                 90    96
   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 2WSD)

(-) Pfam Domains  (3, 4)

Asymmetric/Biological Unit
(-)
Clan: CU_oxidase (192)

(-) 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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  2wsd
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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 2x87 2x88 3zdw 4a66 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