2X88 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HOLOCOTA

Authors :   I. Bento, C. S. Silva, Z. Chen, L. O. Martins, P. F. Lindley, C. M. Soares

Date :   06 Mar 10 (Deposition) - 22 Sep 10 (Release) - 29 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Oxidoreductase, Oxidase, Laccase, Sporulation, Oxygen Reduction, Multicopper-Oxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Bento, C. S. Silva, Z. Chen, L. O. Martins, P. F. Lindley, C. M. Soares
Mechanisms Underlying Dioxygen Reduction In Laccases. Structural And Modelling Studies Focusing On Proton Transfer.
Bmc Struct. Biol. V. 10 29 2010
PubMed-ID: 20822511 | Reference-DOI: 10.1186/1472-6807-10-28

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

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CU	5	Ligand/Ion	COPPER (II) ION
2	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	OXY	1	Ligand/Ion	OXYGEN MOLECULE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:419 , CYS A:492 , HIS A:497 , MET A:502	BINDING SITE FOR RESIDUE CU A 1512
2	AC2	SOFTWARE	HIS A:107 , HIS A:153 , HIS A:493 , OXY A:1516	BINDING SITE FOR RESIDUE CU A 1513
3	AC3	SOFTWARE	HIS A:155 , HIS A:424 , HIS A:491 , OXY A:1516	BINDING SITE FOR RESIDUE CU A 1514
4	AC4	SOFTWARE	HIS A:105 , HIS A:107 , HIS A:422 , HIS A:424 , OXY A:1516 , HOH A:2151	BINDING SITE FOR RESIDUE CU A 1515
5	AC5	SOFTWARE	HIS 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:2525	BINDING SITE FOR RESIDUE OXY A 1516
6	AC6	SOFTWARE	HIS A:86 , HIS A:89 , HOH A:2132 , HOH A:2144	BINDING SITE FOR RESIDUE CU A 1517
7	AC7	SOFTWARE	ALA A:317 , PRO A:328 , ALA A:332 , ASN A:333 , HOH A:2358	BINDING SITE FOR RESIDUE MPD A 1518
8	AC8	SOFTWARE	TYR A:354 , LEU A:355 , SER A:357 , THR A:377 , HOH A:2529	BINDING SITE FOR RESIDUE MPD A 1519
9	AC9	SOFTWARE	PRO A:132 , TYR A:133	BINDING SITE FOR RESIDUE MPD A 1520

Asymmetric/Biological Unit

No.	Residues
1	A:229	-	A:322

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 2X88)

(no "PROSITE Motif" information available for 2X88)

(no "Exon" information available for 2X88)

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:504
 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 d2x88a1 A:2-182 Spore coat protein A, CotA                                                                                                                                           d2x88a2 A:183-356 Spore coat protein A, CotA                                                                                                                                  d2x88a3 A:357-511 Spore coat protein A, CotA                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cu-oxidase-2x88A01 A:175-340                                                                                                                                          -----------------Cu-oxidase_2-2x88A02 A:358-511                                                                                                                             Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------Cu-oxidase_3-2x88A03 A:96-179                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------Cu-oxidase_3-2x88A04 A:96-179                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.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
                 2x88 A   2 TLEKFVDALPIPDTLKPVQQSKEKTYYEVTMEECTHQLHRDLPPTRLWGYNGLFPGPTIEVKRNENVYVKWMNNLPSTHFLPIDHTIH------EEPEVKTVVHLHGGVTPDDSDGYPEAWFSKDFEQTGPYFKREVYHYPNQQRGAILWYHDHAMALTRLNVYAGLVGAYIIHDPKEKRLKLPSDEYDVPLLITDRTINEDGSLFYPSAPENPSPSLPNPSIVPAFCGETILVNGKVWPYLEVEPRKYRFRVINASNTRTYNLSLDNGGDFIQIGSDGGLLPRSVKLNSFSLAPAERYDIIIDFTAYEGESIILANSAGCGGDVNPETDANIMQFRVTKPLAQKDESRKPKYLASYPSVQHERIQNIRTLKLAGTQDEYGRPVLLLNNKRWHDPVTETPKVGTTEIWSIINPTRGTHPIHLHLVSFRVLDRRPFDIARYQESGELSYTGPAVPPPPSEKGWKDTIQAHAGEVLRIAATFGPYSGRYVWHCHILEHEDYDMMRPMDITDP 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     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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Multidomain cupredoxins (146)

Protein domain: Spore coat protein A, CotA (9)

Bacillus subtilis [TaxId: 1423] (9)

1a	d2x88a1	A:2-182
1b	d2x88a2	A:183-356
1c	d2x88a3	A:357-511

(no "CATH Domain" information available for 2X88)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Cu-oxidase (74)

Bacillus subtilis (7)

Cu-oxidase-2x88A01

A:175-340

Family: Cu-oxidase_2 (24)

Bacillus subtilis (7)

Cu-oxidase_2-2x88A02

A:358-511

Family: Cu-oxidase_3 (79)

Bacillus subtilis (7)

3a	Cu-oxidase_3-2x88A03	A:96-179
3b	Cu-oxidase_3-2x88A04	A:96-179

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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		CU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Asn A:221 - Pro A:222	[ RasMol ]
		Gly A:482 - Pro A:483	[ RasMol ]
		Phe A:55 - Pro A:56	[ RasMol ]
		Tyr A:500 - Asp A:501	[ RasMol ]

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	2x88
		Family and Domain Information	:	ProDom \| SYSTERS
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	COTA_BACSU \| P07788
		Comparative Protein Structure Models	:	ModBase
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	COTA_BACSU \| P07788
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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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (3, 4)

Gene Ontology (7, 7)

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