2IWE - JenaLib

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Title :   STRUCTURE OF A CAVITY MUTANT (H117G) OF PSEUDOMONAS AERUGINOSA AZURIN

Authors :   T. E. De Jongh, A. M. M. Van Roon, M. Prudencio, M. Ubbink, G. W. Canters

Date :   29 Jun 06 (Deposition) - 12 Jun 07 (Release) - 28 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.83

Chains :   Asym. Unit : A,D,G,J
Biol. Unit 1: A,J  (1x)
Biol. Unit 2: D,G  (1x)

Keywords :   Blue Copper Protein, Redox Protein, Metal-Binding, Electron Transport, Azurin, Transport, Periplasmic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. E. De Jongh, A. M. M. Van Roon, M. Prudencio, M. Ubbink, G. W. Canter
Click-Chemistry With An Active Site Variant Of Azurin
Eur. J. Inorg. Chem. V. 2006 3861 2006
PubMed: search | Reference-DOI: 10.1002/EJIC.200600574

Molecule 1 - AZURIN
	Chains	:	A, D, G, J
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGK22 (PUC18 DERIVED)
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Other Details	:	DIMERIZED BY COORDINATION OF A BIFUNCTIONAL LIGAND WIRE 1,6-DI(IMIDAZOL-1-YL)HEXANE

		1	2	3	4
Asymmetric Unit	:	A	D	G	J
Biological Unit 1 (1x)	:	A			J
Biological Unit 2 (1x)	:		D	G

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	2IH	2	Ligand/Ion	1,1'-HEXANE-1,6-DIYLBIS(1H-IMIDAZOLE)
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	2IH	1	Ligand/Ion	1,1'-HEXANE-1,6-DIYLBIS(1H-IMIDAZOLE)
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	2IH	1	Ligand/Ion	1,1'-HEXANE-1,6-DIYLBIS(1H-IMIDAZOLE)
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:45 , HIS A:46 , CYS A:112 , MET A:121 , 2IH A:1001	BINDING SITE FOR RESIDUE ZN A1129
2	AC2	SOFTWARE	GLY D:45 , HIS D:46 , CYS D:112 , MET D:121 , 2IH D:1001	BINDING SITE FOR RESIDUE ZN D1129
3	AC3	SOFTWARE	2IH D:1001 , GLY G:45 , HIS G:46 , CYS G:112 , PHE G:114 , MET G:121	BINDING SITE FOR RESIDUE ZN G1129
4	AC4	SOFTWARE	2IH A:1001 , GLY J:45 , HIS J:46 , CYS J:112 , PHE J:114 , MET J:121	BINDING SITE FOR RESIDUE ZN J1129
5	AC5	SOFTWARE	MET A:13 , VAL A:43 , MET A:44 , GLY A:45 , HIS A:46 , CYS A:112 , PHE A:114 , PRO A:115 , GLY A:116 , MET A:121 , ZN A:1129 , VAL J:43 , MET J:44 , GLY J:45 , HIS J:46 , CYS J:112 , PHE J:114 , GLY J:116 , ZN J:1129	BINDING SITE FOR RESIDUE 2IH A1001
6	AC6	SOFTWARE	VAL D:43 , MET D:44 , GLY D:45 , HIS D:46 , CYS D:112 , PHE D:114 , GLY D:116 , ZN D:1129 , MET G:13 , VAL G:43 , MET G:44 , GLY G:45 , HIS G:46 , PHE G:114 , PRO G:115 , GLY G:116 , MET G:121 , ZN G:1129	BINDING SITE FOR RESIDUE 2IH D1001

Asymmetric Unit

No.	Residues
1	A:3	-	A:26
2	D:3	-	D:26
3	G:3	-	G:26
4	J:3	-	J:26

Asymmetric Unit

No.	Residues
1	Ala A:119	-	Leu A:120

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_PSEAE	125-141	4	A:105-121 D:105-121 G:105-121 J:105-121

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_PSEAE	125-141	2	A:105-121 - - J:105-121

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_PSEAE	125-141	2	- D:105-121 G:105-121 -

(no "Exon" information available for 2IWE)

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:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d2iwea_ A: Azurin                                                                                                                SCOP domains
               CATH domains 2iweA00 A:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee.....hhhhhh...eeeehhhhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iwe A   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGGSALMKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D from PDB  Type:PROTEIN  Length:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d2iwed_ D: Azurin                                                                                                                SCOP domains
               CATH domains 2iweD00 D:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee.....hhhhhh...eeee..hhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iwe D   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGGSALMKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain G from PDB  Type:PROTEIN  Length:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d2iweg_ G: Azurin                                                                                                                SCOP domains
               CATH domains 2iweG00 G:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee.....hhhhhh...eeee..hhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iwe G   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGGSALMKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain J from PDB  Type:PROTEIN  Length:128
 aligned with AZUR_PSEAE | P00282 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:128
                                    30        40        50        60        70        80        90       100       110       120       130       140        
           AZUR_PSEAE    21 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALMKGTLTLK 148
               SCOP domains d2iwej_ J: Azurin                                                                                                                SCOP domains
               CATH domains 2iweJ00 J:1-128 Cupredoxins -  blue copper proteins                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeee....eeeeeee.....hhhhhh...eeeehhhhhhhhhhhhhhhhhhh..........ee........eeeeeee.hhh.....eeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iwe J   1 AECSVDIQGNDQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGGSALMKGTLTLK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Plastocyanin/azurin-like (241)

Protein domain: Azurin (95)

Pseudomonas aeruginosa [TaxId: 287] (78)

1a	d2iwea_	A:
1b	d2iwed_	D:
1c	d2iweg_	G:
1d	d2iwej_	J:

Asymmetric 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)

Pseudomonas aeruginosa. Organism_taxid: 287. (21)

1a	2iweA00	A:1-128
1b	2iweD00	D:1-128
1c	2iweG00	G:1-128
1d	2iweJ00	J:1-128

(no "Pfam Domain" information available for 2IWE)

Asymmetric Unit(hide GO term definitions)

Chain A,D,G,J (AZUR_PSEAE | P00282)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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: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:119 - Leu A:120	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	2iwe
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1ag0	STRUCTURE OF CYS 112 ASP AZURIN FROM PSEUDOMONAS AERUGINOSA
1azn	AZURIN MUTANT WITH PHE 114 REPLACED BY ALA (F114A)
1azr	AZURIN MUTANT WITH ASN 47 REPLACED BY ASP (N47D)
1azu	AZURIN
1bex	STRUCTURE OF RUTHENIUM-MODIFIED PSEUDOMONAS AERUGINOSA AZURIN
1cc3	PURPLE CUA CENTER
1e5y	AURIN FROM PSEUDOMONAS AERUGINOSA, REDUCED FORM, PH 5.5
1e5z	AURIN FROM PSEUDOMONAS AERUGINOSA, REDUCED FORM, PH 9.0
1e65	AURIN FROM PSEUDOMONAS AERUGINOSA, APO FORM
1e67	ZN-AZURIN FROM PSEUDOMONAS AERUGINOSA
1etj	AZURIN MUTANT WITH MET 121 REPLACED BY GLU
1ezl	CRYSTAL STRUCTURE OF THE DISULPHIDE BOND- DEFICIENT AZURIN MUTANT C3A/C26A: HOW IMPORTANT IS THE S-S BOND FOR FOLDING AND STABILITY?
1gr7	CRYSTAL STRUCTURE OF THE DOUBLE MUTANT CYS3SER/SER100PRO FROM PSEUDOMONAS AERUGINOSA AT 1.8 E RESOLUTION
1i53	RE(I)-TRICARBONLY DIIMINE (Q107H)) AZURIN
1ils	MOL_ID: 1; MOLECULE: AZURIN; CHAIN: A, B, C, D; ENGINEERED: YES; MUTATION: I7S
1ilu	MOL_ID: 1; MOLECULE: AZURIN; CHAIN: A, B, C, D, E, F, G, H, I, K, L, M; ENGINEERED: YES; MUTATION: F110S
1jvl	AZURIN DIMER, COVALENTLY CROSSLINKED THROUGH BIS-MALEIMIDOMETHYLETHER
1jvo	AZURIN DIMER, CROSSLINKED VIA DISULFIDE BRIDGE
1jze	PSEUDOMONAS AERUGINOSA AZURIN RU(BPY)2(IM)( HIS83)
1jzf	PSEUDOMONAS AERUGINOSA OXIDIZED AZURIN(CU2+) RU(TPY)(PHEN)(HIS83)
1jzg	PSEUDOMONAS AERUGINOSA REDUCED AZURIN (CU1+) RU(TPY)(PHEN)(HIS83)
1jzh	PSEUDOMONAS AERUGINOSA AZURIN RU(TPY)(BPY)( HIS83)
1jzi	PSEUDOMONAS AERUGINOSA AZURIN RE(PHEN)(CO)3 (HIS83)
1jzj	PSEUDOMONAS AERUGINOSA AZURIN OS(BPY)2(IM)( HIS83)
1nzr	AZURIN MUTANT WITH TRP 48 REPLACED BY MET (W48M)
1r1c	PSEUDOMONAS AERUGINOSA W48F/Y72F/H83Q/Y108W- AZURIN RE(PHEN)(CO)3(HIS107)
1vlx	STRUCTURE OF ELECTRON TRANSFER (COBALT-PROTEIN )
1xb3	THE D62C/K74C DOUBLE MUTANT OF PSEUDOMONAS AERUGINOSA AZURIN
1xb6	THE K24R MUTANT OF PSEUDOMONAS AERUGINOSA AZURIN
1xb8	ZN SUBSTITUTED FORM OF D62C/K74C DOUBLE MUTANT OFPSEUDOMONAS AERUGINOSA AZURIN
2azu	AZURIN MUTANT WITH HIS 35 REPLACED BY LEU (H35L)
2tsa	AZURIN MUTANT M121A
2tsb	AZURIN MUTANT M121A-AZIDE
3azu	AZURIN MUTANT WITH HIS 35 REPLACED BY GLN (H35Q)
4azu	AZURIN (PH 5.5)
5azu	AZURIN (PH 9.0)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (4, 4)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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