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Description

Title :   STRUCTURE OF THE REDUCED FORM OF THE P94A MUTANT OF AMICYANIN

Authors :   C. J. Carrell, D. Sun, S. Jiang, V. L. Davidson, F. S. Mathews

Date :   19 Feb 04 (Deposition) - 27 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.05

Chains :   Asym./Biol. Unit : A

Keywords :   Blue Copper Protein, Beta Sandwich, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. J. Carrell, D. Sun, S. Jiang, V. L. Davidson, F. S. Mathews
Structural Studies Of Two Mutants Of Amicyanin From Paracoccus Denitrificans That Stabilize The Reduced State Of The Copper.
Biochemistry V. 43 9372 2004
PubMed-ID: 15260480 | Reference-DOI: 10.1021/BI049634Z
(for further references see the PDB file header)

Compounds

Molecule 1 - AMICYANIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	MAUC, AMI
	Mutation	:	YES
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 3)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CU1	1	Ligand/Ion	COPPER (I) ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:52 , HIS A:53 , CYS A:92 , HIS A:95 , MET A:98 , HOH A:351	BINDING SITE FOR RESIDUE CU1 A 107
2	AC2	SOFTWARE	ALA A:26 , LYS A:27 , GLU A:31 , LYS A:68 , THR A:93 , HOH A:248	BINDING SITE FOR RESIDUE PO4 A 111
3	AC3	SOFTWARE	LYS A:29 , GLU A:31 , HOH A:213 , HOH A:226 , HOH A:248 , HOH A:289	BINDING SITE FOR RESIDUE PO4 A 112

SS Bonds (0, 0)

(no "SS Bond" information available for 1SF3)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1SF3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1SF3)

PROSITE Motifs (1, 1)

Asymmetric/Biological 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:85-98

Exons (0, 0)

(no "Exon" information available for 1SF3)

Sequences/Alignments

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: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 d1sf3a_ A: Amicyanin                                                                                      SCOP domains
               CATH domains 1sf3A00 A:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains ----------------Copper-bind-1sf3A01 A:17-105                                                              Pfam domains
         Sec.struct. author ..ee......ee.hhh....eeeeee..ee...eeee....eeeeee........ee.........ee.......eeeeeee...eeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1sf3 A   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTAHPFMRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Plastocyanin/azurin-like (241)

Protein domain: Amicyanin (34)

Paracoccus denitrificans [TaxId: 266] (33)

d1sf3a_

CATH Domains (1, 1)

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)

Paracoccus denitrificans. Organism_taxid: 266. (20)

1sf3A00

A:1-105

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Copper-bind (82)

Paracoccus denitrificans (11)

Copper-bind-1sf3A01

A:17-105

Gene Ontology (5, 5)

Asymmetric/Biological 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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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	AMCY_PARDE \| P22364	:	1aac 1aaj 1aan 1bxa 1mda 1mg2 1mg3 1sf5 1sfd 1sfh 1t5k 2gb2 2gba 2gc4 2gc7 2idq 2ids 2idt 2idu 2j55 2j56 2j57 2mta 2ov0 2qdv 2qdw 2rac 3ie9 3iea 3l45 3ply 3rym 4p5r 4p5s

Related Entries Specified in the PDB File

1sf5	STRUCTURE OF OXIDIZED STATE OF THE P94A MUTANT OF AMICYANIN
1sfd	OXIDIZED FORM OF AMICYANIN MUTANT P94F
1sfh	REDUCED STATE OF AMICYANIN MUTANT P94F