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(-) Description

Title :  3D STRUCTURE OF COTA INCUBATED WITH SODIUM AZIDE
 
Authors :  I. Bento, L. O. Martins, G. G. Lopes, M. A. Carrondo, P. F. Lindley
Date :  24 Aug 04  (Deposition) - 26 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Multicopper-Oxidase, Laccase, Oxygen Reduction, Oxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Bento, L. O. Martins, G. G. Lopes, M. A. Carrondo, P. F. Lindley
Dioxygen Reduction By Multi-Copper Oxidases; A Structural Perspective.
Dalton Trans. V. 7 3507 2005
PubMed-ID: 16234932  |  Reference-DOI: 10.1039/B504806K

(-) Compounds

Molecule 1 - SPORE COAT PROTEIN A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: COTA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1AZI1Ligand/IonAZIDE ION
2CU4Ligand/IonCOPPER (II) ION
3GOL2Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:419 , CYS A:492 , HIS A:497 , MET A:502BINDING SITE FOR RESIDUE CU A1511
2AC2SOFTWAREHIS A:107 , HIS A:153 , HIS A:493 , AZI A:1515BINDING SITE FOR RESIDUE CU A1512
3AC3SOFTWAREHIS A:155 , HIS A:424 , HIS A:491 , AZI A:1515BINDING SITE FOR RESIDUE CU A1513
4AC4SOFTWAREHIS A:105 , HIS A:107 , HIS A:422 , HIS A:424 , AZI A:1515 , HOH A:2143BINDING SITE FOR RESIDUE CU A1514
5AC5SOFTWAREHIS A:105 , HIS A:107 , HIS A:153 , HIS A:155 , HIS A:422 , HIS A:424 , HIS A:491 , HIS A:493 , GLU A:498 , CU A:1512 , CU A:1513 , CU A:1514BINDING SITE FOR RESIDUE AZI A1515
6AC6SOFTWAREASP A:113 , ASP A:114 , TYR A:118 , ALA A:121 , TYR A:133 , LYS A:135 , HOH A:2156 , HOH A:2474BINDING SITE FOR RESIDUE GOL A1516
7AC7SOFTWARELYS A:25 , VAL A:138 , THR A:307 , ALA A:308 , TYR A:309 , GLU A:310 , HOH A:2475BINDING SITE FOR RESIDUE GOL A1517

(-) 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 1W6W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W6W)

(-) Exons   (0, 0)

(no "Exon" information available for 1W6W)

(-) 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:503
 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 d1w6wa1 A:2-182 Spore coat protein A, CotA                                                                                                                                           d1w6wa2 A:183-356 Spore coat protein A, CotA                                                                                                                                  d1w6wa3 A:357-511 Spore coat protein A, CotA                                                                                                                SCOP domains
               CATH domains 1w6wA01 A:2-175 Cupredoxins -  blue copper proteins                                                                                                                           1w6wA02 A:176-356 Cupredoxins -  blue copper proteins                                                                                                                                1w6wA03 A:357-511 Cupredoxins -  blue copper proteins                                                                                                       CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cu-oxidase-1w6wA01 A:175-340                                                                                                                                          -----------------Cu-oxidase_2-1w6wA02 A:358-511                                                                                                                             Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------Cu-oxidase_3-1w6wA03 A:97-179                                                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------Cu-oxidase_3-1w6wA04 A:97-179                                                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ..................ee....eeeeeeeeeeee........eeeeee........eeee....eeeeeee..........hhhhh-------.......eeee....hhhhh.......hhhhh.........eeee......eeeeeee....hhhhhhhh..eeeeeeehhhhhhhh..hhh.eeeeeeeeeee.....ee........................eeee..ee..eee....eeeeeeee......eeeee.....eeeeee..eeeeeeeee..eee....eeeeeee.hhhh..eeeeee..............eeeeee...................hhhhh...eeeeeeeeeeeee.....eeeee.................eeeeeeee.....eeeee....eeeeeeee.hhhhhhhhh...........hhhhh....eeee...eeeeeeee.....eeeeeee.hhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1w6w A   2 TLEKFVDALPIPDTLKPVQQSKEKTYYEVTMEECTHQLHRDLPPTRLWGYNGLFPGPTIEVKRNENVYVKWMNNLPSTHFLPIDHTIH-------EPEVKTVVHLHGGVTPDDSDGYPEAWFSKDFEQTGPYFKREVYHYPNQQRGAILWYHDHAMALTRLNVYAGLVGAYIIHDPKEKRLKLPSDEYDVPLLITDRTINEDGSLFYPSAPENPSPSLPNPSIVPAFCGETILVNGKVWPYLEVEPRKYRFRVINASNTRTYNLSLDNGGDFIQIGSDGGLLPRSVKLNSFSLAPAERYDIIIDFTAYEGESIILANSAGCGGDVNPETDANIMQFRVTKPLAQKDESRKPKYLASYPSVQHERIQNIRTLKLAGTQDEYGRPVLLLNNKRWHDPVTETPKVGTTEIWSIINPTRGTHPIHLHLVSFRVLDRRPFDIARYQESGELSYTGPAVPPPPSEKGWKDTIQAHAGEVLRIAATFGPYSGRYVWHCHILEHEDYDMMRPMDITDP 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       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511
                                                                                                                  89      97
   Legend:   → Mismatch (orange background)
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  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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) 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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  1w6w
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  COTA_BACSU | P07788
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 Related Entries

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

UniProtKB/Swiss-Prot
        COTA_BACSU | P07788: 1gsk 1of0 1w6l 1w8e 2bhf 2wsd 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
1hkp CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER 1H SOAKING WITH SYRINGALDAZINE (SGZ)
1hkz CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER 8H SOAKING WITH ABTS
1hl0 CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER 20H SOAKING WITH SYRINGALDAZINE (SGZ)
1hl1 CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER20H SOAKING WITH ABTS
1of0 CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER 1H SOAKING WITH ABTS
1ogr CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER 6H SOAKING WITH ABTS
1uvw BACILLUS SUBTILIS COTA LACCASE ADDUCT WITH ABTS
1w6l 3D STRUCTURE OF COTA INCUBATED WITH CUCL2
1w8e 3D STRUCTURE OF COTA INCUBATED WITH HYDROGEN PEROXIDE