1PF3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE M441L MUTANT OF THE MULTICOPPER OXIDASE CUEO

Authors :   S. A. Roberts, G. F. Wildner, G. Grass, A. Weichsel, A. Ambrus, C. Rensing, W. R. Montfort

Date :   23 May 03 (Deposition) - 24 Jun 03 (Release) - 17 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

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

Reference :   S. A. Roberts, G. F. Wildner, G. Grass, A. Weichsel, A. Ambrus, C. Rensing, W. R. Montfort
A Labile Regulatory Copper Ion Lies Near The T1 Copper Site In The Multicopper Oxidase Cueo.
J. Biol. Chem. V. 278 31958 2003
PubMed-ID: 12794077 | Reference-DOI: 10.1074/JBC.M302963200
(for further references see the PDB file header)

Molecule 1 - BLUE COPPER OXIDASE CUEO
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Gene	:	CUEO
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	COPPER EFFLUX OXIDASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	C2C	1	Ligand/Ion	CU-CL-CU LINKAGE
2	CU	2	Ligand/Ion	COPPER (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:442 , 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 , C2C A:702 , HOH A:2018	BINDING SITE FOR RESIDUE CU A 703
3	AC3	SOFTWARE	HIS A:101 , HIS A:103 , TRP A:139 , HIS A:141 , HIS A:143 , HIS A:446 , HIS A:448 , HIS A:499 , HIS A:501 , CU A:703 , HOH A:2324	BINDING SITE FOR RESIDUE C2C A 702

(no "SS Bond" information available for 1PF3)

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 1PF3)

Asymmetric/Biological Unit (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

(no "Exon" information available for 1PF3)

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:463
 aligned with CUEO_ECOLI | P36649 from UniProtKB/Swiss-Prot  Length:516

    Alignment length:486
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510      
           CUEO_ECOLI    31 RPTLPIPDLLTTDARNRIQLTIGAGQSTFGGKTATTWGYNGNLLGPAVKLQRGKAVTVDIYNQLTEETTLHWHGLEVPGEVDGGPQGIIPPGGKRSVTLNVDQPAATCWFHPHQHGKTGRQVAMGLAGLVVIEDDEILKLMLPKQWGIDDVPVIVQDKKFSADGQIDYQLDVMTAAVGWFGDTLLTNGAIYPQHAAPRGWLRLRLLNGCNARSLNFATSDNRPLYVIASDGGLLPEPVKVSELPVLMGERFEVLVEVNDNKPFDLVTLPVSQMGMAIAPFDKPHPVMRIQPIAISASGALPDTLSSLPALPSLEGLTVRKLQLSMDPMLDMMGMQMLMEKYGDQAMAGMDHSQMMGHMGHGNMNHMNHGGKFDFHHANKINGQAFDMNKPMFAAAKGQYERWVISGVGDMMLHPFHIHGTQFRILSENGKPPAAHRAGWKDTVKVEGNVSEVLVKFNHDAPKEHAYMAHCHLLEHEDTGMMLGFTV 516
               SCOP domains d1pf3a1 A:31-170 multi-copper oxidase CueO                                                                                                  d1pf3a2 A:171-335 multi-copper oxidase CueO                                                                                                                          d1pf3a3 A:336-516 multi-copper oxidase CueO                                                                                                                                           SCOP domains
               CATH domains 1pf3A01 A:31-174 Cupredoxins -  blue copper proteins                                                                                            1pf3A02 A:175-326 Cupredoxins -  blue copper proteins                                                                                                   ------------------1pf3A03 A:345-516 Cupredoxins -  bl                       ue copper proteins                                                                                                 CATH domains
               Pfam domains --------------------Cu-oxidase_3-1pf3A03 A:51-167                                                                                        --------------Cu-oxidase-1pf3A01 A:182-312                                                                                                       ------------------------------------------------------------Cu-oxid                       ase_2-1pf3A02 A:373-516                                                                                            Pfam domains
         Sec.struct. author ........ee......eeeeeeeeeeeee..eeeeeeee.......eeeee...eeeeeeee........eee....hhhhhh..........eeeeeee.....eeeeee.....hhhhhhhh...eeeeeehhhhhh..........eeeeeeeee............hhhhhhhh....eeee......eeeeeeeeeeeeeee......eeeee.....eeeeee..eeeeeeeee..eee....eeeeeeee.....eeeee................eeeeeeeeeeee.....................eeeeeeeeehhhhhhhhhhhhhhhhhhhhhh..-----------------------hhhh.eee...........ee......eeeeee.......eeeee.....eeee......hhhhh....eeee...eeeeee......hhhhheeeee.hhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pf3 A  31 RPTLPIPDLLTTDARNRIQLTIGAGQSTFGGKTATTWGYNGNLLGPAVKLQRGKAVTVDIYNQLTEETTLHWHGLEVPGEVDGGPQGIIPPGGKRSVTLNVDQPAATCWFHPHQHGKTGRQVAMGLAGLVVIEDDEILKLMLPKQWGIDDVPVIVQDKKFSADGQIDYQLDVMTAAVGWFGDTLLTNGAIYPQHAAPRGWLRLRLLNGCNARSLNFATSDNRPLYVIASDGGLLPEPVKVSELPVLMGERFEVLVEVNDNKPFDLVTLPVSQMGMAIAPFDKPHPVMRIQPIAISASGALPDTLSSLPALPSLEGLTVRKLQLSMDPMLDMMGMQMLMEKYGDQAMAGM-----------------------DFHHANKINGQAFDMNKPMFAAAKGQYERWVISGVGDMLLHPFHIHGTQFRILSENGKPPAAHRAGWKDTVKVEGNVSEVLVKFNHDAPKEHAYMAHCHLLEHEDTGMMLGFTV 516
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370        |-         -         -  |    410       420       430       440       450       460       470       480       490       500       510      
                                                                                                                                                                                                                                                                                                                                                                                      379                     403

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: multi-copper oxidase CueO (29)

Escherichia coli [TaxId: 562] (29)

1a	d1pf3a1	A:31-170
1b	d1pf3a2	A:171-335
1c	d1pf3a3	A:336-516

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Escherichia coli. Organism_taxid: 562. (2)

1a	1pf3A01	A:31-174
1b	1pf3A03	A:345-516
1c	1pf3A02	A:175-326

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Cu-oxidase (74)

Escherichia coli (strain K12) (5)

Cu-oxidase-1pf3A01

A:182-312

Family: Cu-oxidase_2 (24)

Escherichia coli (strain K12) (5)

Cu-oxidase_2-1pf3A02

A:373-516

Family: Cu-oxidase_3 (79)

Escherichia coli (strain K12) (5)

Cu-oxidase_3-1pf3A03

A:51-167

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		C2C	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1pf3
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CUEO_ECOLI \| P36649
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CUEO_ECOLI \| P36649
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (3, 3)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File