2YXV - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE DELETION MUTANT OF MULTICOPPER OXIDASE CUEO

Authors :   Y. Higuchi, H. Komori

Date :   27 Apr 07 (Deposition) - 01 Jan 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Multicopper Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kataoka, H. Komori, Y. Ueki, Y. Konno, Y. Kamitaka, S. Kurose, S. Tsujimura, Y. Higuchi, K. Kano, D. Seo, T. Sakurai
Structure And Function Of The Engineered Multicopper Oxidas Cueo From Escherichia Coli--Deletion Of The Methionine-Rich Helical Region Covering The Substrate-Binding Site
J. Mol. Biol. V. 373 141 2007
PubMed-ID: 17804014 | Reference-DOI: 10.1016/J.JMB.2007.07.041

Molecule 1 - BLUE COPPER OXIDASE CUEO
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 (NOVAGEN)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	JM109
	Synonym	:	COPPER EFFLUX OXIDASE, MULTICOPPER OXIDASE CUEO

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	C2O	2	Ligand/Ion	CU-O-CU LINKAGE
2	CU	4	Ligand/Ion	COPPER (II) ION
3	NO3	1	Ligand/Ion	NITRATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	C2O	1	Ligand/Ion	CU-O-CU LINKAGE
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	NO3	1	Ligand/Ion	NITRATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	C2O	1	Ligand/Ion	CU-O-CU LINKAGE
2	CU	-1	Ligand/Ion	COPPER (II) ION
3	NO3	-1	Ligand/Ion	NITRATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:443 , CYS A:500 , HIS A:505 , MET A:510	BINDING SITE FOR RESIDUE CU A 701
2	AC2	SOFTWARE	HIS A:101 , HIS A:103 , HIS A:446 , HIS A:448 , C2O A:702 , HOH A:745	BINDING SITE FOR RESIDUE CU A 703
3	AC3	SOFTWARE	HIS B:443 , CYS B:500 , HIS B:505 , MET B:510	BINDING SITE FOR RESIDUE CU B 701
4	AC4	SOFTWARE	HIS B:101 , HIS B:103 , HIS B:446 , HIS B:448 , C2O B:702 , HOH B:748	BINDING SITE FOR RESIDUE CU B 703
5	AC5	SOFTWARE	MET A:303 , GLY A:304 , MET A:305 , ALA A:306 , ILE A:307 , GLN B:302 , MET B:303 , GLY B:304 , MET B:305 , ALA B:306 , HOH B:841	BINDING SITE FOR RESIDUE NO3 A 706
6	AC6	SOFTWARE	HIS A:101 , HIS A:103 , HIS A:141 , HIS A:143 , HIS A:446 , HIS A:448 , HIS A:499 , HIS A:501 , CU A:703	BINDING SITE FOR RESIDUE C2O A 702
7	AC7	SOFTWARE	HIS B:101 , HIS B:103 , HIS B:141 , HIS B:143 , HIS B:446 , HIS B:448 , HIS B:499 , HIS B:501 , CU B:703	BINDING SITE FOR RESIDUE C2O B 702

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

Asymmetric Unit

No.	Residues
1	Ala A:308	-	Pro A:309
2	Ala B:308	-	Pro B:309

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTICOPPER_OXIDASE2	PS00080	Multicopper oxidases signature 2.	CUEO_ECOLI	499-510	2	A:499-510 B:499-510

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTICOPPER_OXIDASE2	PS00080	Multicopper oxidases signature 2.	CUEO_ECOLI	499-510	1	A:499-510 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTICOPPER_OXIDASE2	PS00080	Multicopper oxidases signature 2.	CUEO_ECOLI	499-510	1	- B:499-510

(no "Exon" information available for 2YXV)

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:444
 aligned with CUEO_ECOLI | P36649 from UniProtKB/Swiss-Prot  Length:516

    Alignment length:492
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                516     
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509      |  -  
           CUEO_ECOLI    30 ERPTLPIPDLLTTDARNRIQLTIGAGQSTFGGKTATTWGYNGNLLGPAVKLQRGKAVTVDIYNQLTEETTLHWHGLEVPGEVDGGPQGIIPPGGKRSVTLNVDQPAATCWFHPHQHGKTGRQVAMGLAGLVVIEDDEILKLMLPKQWGIDDVPVIVQDKKFSADGQIDYQLDVMTAAVGWFGDTLLTNGAIYPQHAAPRGWLRLRLLNGCNARSLNFATSDNRPLYVIASDGGLLPEPVKVSELPVLMGERFEVLVEVNDNKPFDLVTLPVSQMGMAIAPFDKPHPVMRIQPIAISASGALPDTLSSLPALPSLEGLTVRKLQLSMDPMLDMMGMQMLMEKYGDQAMAGMDHSQMMGHMGHGNMNHMNHGGKFDFHHANKINGQAFDMNKPMFAAAKGQYERWVISGVGDMMLHPFHIHGTQFRILSENGKPPAAHRAGWKDTVKVEGNVSEVLVKFNHDAPKEHAYMAHCHLLEHEDTGMMLGFTV-----   -
               SCOP domains d2yxva1 A:30-170 automated matches                                                                                                           d2yxva2 A:171-335 automated matches                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........ee......eeeeeeeeeeeee..eeeeeeee.......eeeee....eeeeeee........eee....hhhhh...........eeeeee......eeeeee.....hhhhhhhhh..eeeeeehhhhhh..........eeeeeeeee............hhhhhhhh....eeee..ee..eeeee.eeeeeeeee......eeeee.....eeeeee..eeeeeeeee..eee....eeeeeeee.....eeeee................eeeeeeeee........................eeeeeeeeee.------------------------------------------------.eeee...........eee.....eeeeee.......eeeee.....eeee......hhhhh....eeee...eeeeee......hhhhheeeee.hhhhhhh..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yxv A  30 ERPTLPIPDLLTTDARNRIQLTIGAGQSTFGGKTATTWGYNGNLLGPAVKLQRGKAVTVDIYNQLTEETTLHWHGLEVPGEVDGGPQGIIPPGGKRSVTLNVDQPAATCWFHPHQHGKTGRQVAMGLAGLVVIEDDEILKLMLPKQWGIDDVPVIVQDKKFSADGQIDYQLDVMTAAVGWFGDTLLTNGAIYPQHAAPRGWLRLRLLNGCNARSLNFATSDNRPLYVIASDGGLLPEPVKVSELPVLMGERFEVLVEVNDNKPFDLVTLPVSQMGMAIAPFDKPHPVMRIQPIAISASGALPDTLSSLPALPSLEGLTVRKLQLSMDG------------------------------------------------GANKINGQAFDMNKPMFAAAKGQYERWVISGVGDMMLHPFHIHGTQFRILSENGKPPAAHRAGWKDTVKVEGNVSEVLVKFNHDAPKEHAYMAHCHLLEHEDTGMMLGFTVGHHHH 521
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       | -         -         -         -         -      |409       419       429       439       449       459       469       479       489       499       509       519  
                                                                                                                                                                                                                                                                                                                                                                 357                                              406

Chain B from PDB  Type:PROTEIN  Length:440
 aligned with CUEO_ECOLI | P36649 from UniProtKB/Swiss-Prot  Length:516

    Alignment length:488
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                516 
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509      | 
           CUEO_ECOLI    30 ERPTLPIPDLLTTDARNRIQLTIGAGQSTFGGKTATTWGYNGNLLGPAVKLQRGKAVTVDIYNQLTEETTLHWHGLEVPGEVDGGPQGIIPPGGKRSVTLNVDQPAATCWFHPHQHGKTGRQVAMGLAGLVVIEDDEILKLMLPKQWGIDDVPVIVQDKKFSADGQIDYQLDVMTAAVGWFGDTLLTNGAIYPQHAAPRGWLRLRLLNGCNARSLNFATSDNRPLYVIASDGGLLPEPVKVSELPVLMGERFEVLVEVNDNKPFDLVTLPVSQMGMAIAPFDKPHPVMRIQPIAISASGALPDTLSSLPALPSLEGLTVRKLQLSMDPMLDMMGMQMLMEKYGDQAMAGMDHSQMMGHMGHGNMNHMNHGGKFDFHHANKINGQAFDMNKPMFAAAKGQYERWVISGVGDMMLHPFHIHGTQFRILSENGKPPAAHRAGWKDTVKVEGNVSEVLVKFNHDAPKEHAYMAHCHLLEHEDTGMMLGFTV-   -
               SCOP domains d2yxvb1 B:30-170 automated matches                                                                                                           d2yxvb2 B:171-335 automated matches                                                                                                                                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------Cu-oxidase_3-2yxvB05 B:51-167                                                                                        --------------Cu-oxidase-2yxvB01 B:182-312                                                                                                       ---------------------------------------------------------------------------------------------Cu-oxidase_2-2yxvB03 B:406-516                                                                                 - Pfam domains (1)
           Pfam domains (2) ---------------------Cu-oxidase_3-2yxvB06 B:51-167                                                                                        --------------Cu-oxidase-2yxvB02 B:182-312                                                                                                       ---------------------------------------------------------------------------------------------Cu-oxidase_2-2yxvB04 B:406-516                                                                                 - Pfam domains (2)
         Sec.struct. author .........ee......eeeeeeeeeeeee..eeeeeeee.......eeeee...eeeeeeee........eee....hhhhh...........eeeeeee.....eeeeee.....hhhhhhhhh..eeeeeehhhhhh..........eeeeeeeee............hhhhhhhh....eeee......eeeeeeeeeeeeeee......eeeee.....eeeeee..eeeeeeeee..eee....eeeeeeee.....eeeee................eeeeeeeeeeee.....................eeeeeeeeee.------------------------------------------------.eeee...........eeee....eeeeee.......eeeee.....eeee......hhhhh....eeee...eeeeee......hhhhheeeee.hhhhhhh..eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yxv B  30 ERPTLPIPDLLTTDARNRIQLTIGAGQSTFGGKTATTWGYNGNLLGPAVKLQRGKAVTVDIYNQLTEETTLHWHGLEVPGEVDGGPQGIIPPGGKRSVTLNVDQPAATCWFHPHQHGKTGRQVAMGLAGLVVIEDDEILKLMLPKQWGIDDVPVIVQDKKFSADGQIDYQLDVMTAAVGWFGDTLLTNGAIYPQHAAPRGWLRLRLLNGCNARSLNFATSDNRPLYVIASDGGLLPEPVKVSELPVLMGERFEVLVEVNDNKPFDLVTLPVSQMGMAIAPFDKPHPVMRIQPIAISASGALPDTLSSLPALPSLEGLTVRKLQLSMDG------------------------------------------------GANKINGQAFDMNKPMFAAAKGQYERWVISGVGDMMLHPFHIHGTQFRILSENGKPPAAHRAGWKDTVKVEGNVSEVLVKFNHDAPKEHAYMAHCHLLEHEDTGMMLGFTVG 517
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       | -         -         -         -         -      |409       419       429       439       449       459       469       479       489       499       509        
                                                                                                                                                                                                                                                                                                                                                                 357                                              406

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: automated matches (57)

Protein domain: automated matches (57)

Escherichia coli [TaxId: 562] (2)

1a	d2yxva1	A:30-170
1b	d2yxva2	A:171-335
1c	d2yxvb1	B:30-170
1d	d2yxvb2	B:171-335

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Cu-oxidase (74)

Escherichia coli (strain K12) (5)

1a	Cu-oxidase-2yxvB01	B:182-312
1b	Cu-oxidase-2yxvB02	B:182-312

Family: Cu-oxidase_2 (24)

Escherichia coli (strain K12) (5)

2a	Cu-oxidase_2-2yxvB03	B:406-516
2b	Cu-oxidase_2-2yxvB04	B:406-516

Family: Cu-oxidase_3 (79)

Escherichia coli (strain K12) (5)

3a	Cu-oxidase_3-2yxvB05	B:51-167
3b	Cu-oxidase_3-2yxvB06	B:51-167

Asymmetric Unit(hide GO term definitions)

Chain A,B (CUEO_ECOLI | P36649)

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.
	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.
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.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:308 - Pro A:309	[ RasMol ]
		Ala B:308 - Pro B:309	[ RasMol ]

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	2yxv
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2yxw	THE SAME PROTEIN AT 1.5 A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (8, 8)

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