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Title :   STRUCTURE OF OXIDIZED M98L MUTANT OF AMICYANIN

Authors :   N Sukumar, V. L. Davidson

Date :   22 Jul 09 (Deposition) - 06 Oct 09 (Release) - 13 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (6x)
Biol. Unit 3: A  (3x)

Keywords :   Type-I Blue Copper Protein; Beta Sandwich, Electron Transport, Copper, Metal-Binding, Periplasm, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Choi, N. Sukumar, A. Liu, V. L. Davidson
Defining The Role Of The Axial Ligand Of The Type 1 Copper Site In Amicyanin By Replacement Of Methionine With Leucine.
Biochemistry V. 48 9174 2009
PubMed-ID: 19715303 | Reference-DOI: 10.1021/BI900836H
(for further references see the PDB file header)

Compounds

Molecule 1 - AMICYANIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMEG
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 27-131
	Gene	:	AMI, MAUC
	Mutation	:	YES
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	CU	1	Ligand/Ion	COPPER (II) ION
4	PO4	1	Ligand/Ion	PHOSPHATE ION
5	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	CU	-1	Ligand/Ion	COPPER (II) ION
4	PO4	1	Ligand/Ion	PHOSPHATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	ACT	6	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	CU	-1	Ligand/Ion	COPPER (II) ION
4	PO4	6	Ligand/Ion	PHOSPHATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	CU	-1	Ligand/Ion	COPPER (II) ION
4	PO4	3	Ligand/Ion	PHOSPHATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	1	A:85-97

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	1	A:85-97

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	6	A:85-97

Biological Unit 3 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AMCY_PARDE	111-124	3	A:85-97

Exons (0, 0)

Sequences/Alignments

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

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Chain A from PDB  Type:PROTEIN  Length:105
 aligned with AMCY_PARDE | P22364 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:105
                                    36        46        56        66        76        86        96       106       116       126     
           AMCY_PARDE    27 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE 131
               SCOP domains d3ie9a_ A: Amicyanin                                                                                      SCOP domains
               CATH domains 3ie9A00 A:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhh....eeeeee..ee...eeee....eeeeee........ee.........ee.......eeeeeee...eeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3ie9 A   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFLRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

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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, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A (AMCY_PARDE | P22364)

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.
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).

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