3PLY - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF OXIDIZED P96G MUTANT OF AMICYANIN

Authors :   N. Sukumar, V. L. Davidson

Date :   15 Nov 10 (Deposition) - 09 Feb 11 (Release) - 02 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

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

Reference :   M. Choi, N. Sukumar, F. S. Mathews, A. Liu, V. L. Davidson
Proline 96 Of The Copper Ligand Loop Of Amicyanin Regulates Electron Transfer From Methylamine Dehydrogenase By Positioning Other Residues At The Protein-Protein Interface
Biochemistry V. 50 1265 2011
PubMed-ID: 21268585 | Reference-DOI: 10.1021/BI101794Y

Molecule 1 - AMICYANIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMEG
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 27-131
	Gene	:	AMI, MAUC
	Mutation	:	YES
	Organism Scientific	:	PARACOCCUS DENITRIFICANS
	Organism Taxid	:	266

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION
2	K	1	Ligand/Ion	POTASSIUM ION
3	NA	2	Ligand/Ion	SODIUM ION
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	K	-1	Ligand/Ion	POTASSIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	K	-1	Ligand/Ion	POTASSIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	K	-1	Ligand/Ion	POTASSIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	K	-1	Ligand/Ion	POTASSIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:53 , CYS A:92 , HIS A:95 , MET A:98	BINDING SITE FOR RESIDUE CU A 106
2	AC2	SOFTWARE	SER A:7 , TYR A:78 , SER A:79	BINDING SITE FOR RESIDUE NA A 107
3	AC3	SOFTWARE	PHE A:57 , VAL A:58 , VAL A:61 , LEU A:62 , ALA A:65 , LEU A:67	BINDING SITE FOR RESIDUE NA A 108
4	AC4	SOFTWARE	HIS B:53 , CYS B:92 , HIS B:95 , MET B:98	BINDING SITE FOR RESIDUE CU B 106
5	AC5	SOFTWARE	HIS C:53 , CYS C:92 , HIS C:95 , MET C:98	BINDING SITE FOR RESIDUE CU C 106
6	AC6	SOFTWARE	GLU C:49 , ALA C:50 , HOH C:130 , LYS D:29	BINDING SITE FOR RESIDUE PO4 C 107
7	AC7	SOFTWARE	ALA B:65 , HIS C:36 , HOH C:151	BINDING SITE FOR RESIDUE PO4 C 108
8	AC8	SOFTWARE	GLY B:60 , HOH B:110 , VAL C:22 , THR C:32	BINDING SITE FOR RESIDUE K C 109
9	AC9	SOFTWARE	HIS D:53 , CYS D:92 , HIS D:95 , MET D:98	BINDING SITE FOR RESIDUE CU D 106

(no "SS Bond" information available for 3PLY)

(no "Cis Peptide Bond" information available for 3PLY)

(no "SAP(SNP)/Variant" information available for 3PLY)

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.	AMCY_PARDE	111-124	4	A:85-98 B:85-98 C:85-98 D:85-98

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:85-98 - - -

Biological Unit 2 (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	- B:85-98 - -

Biological Unit 3 (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	- - C:85-98 -

Biological Unit 4 (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	- - - D:85-98

(no "Exon" information available for 3PLY)

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: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 d3plya_ A: Amicyanin                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhh....eeeeee..ee...eeeee...eeeeee........ee.........ee.......eeeeeee...eeeeee.......eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3ply A   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHGFMRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

Chain B 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 d3plyb_ B: Amicyanin                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhh....eeeeee..ee...eeeee...eeeeee........ee.........ee.......eeeeeee...eeeeee.......eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3ply B   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHGFMRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

Chain C 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 d3plyc_ C: Amicyanin                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- 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
                 3ply C   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHGFMRGKVVVE 105
                                    10        20        30        40        50        60        70        80        90       100

Chain D 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 d3plyd_ D: Amicyanin                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------Copper-bind-3plyD01 D:17-105                                                              Pfam domains (1)
           Pfam domains (2) ----------------Copper-bind-3plyD02 D:17-105                                                              Pfam domains (2)
           Pfam domains (3) ----------------Copper-bind-3plyD03 D:17-105                                                              Pfam domains (3)
           Pfam domains (4) ----------------Copper-bind-3plyD04 D:17-105                                                              Pfam domains (4)
         Sec.struct. author ..ee................eeeeee..ee...eeee.....eeeee........ee.........ee.........eeeee...eee..ee..eeeee.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------COPPER_BLUE   ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3ply D   1 DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHGFMRGKVVVE 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 '\|'

Asymmetric 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)

1a	d3plya_	A:
1b	d3plyb_	B:
1c	d3plyc_	C:
1d	d3plyd_	D:

(no "CATH Domain" information available for 3PLY)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Copper-bind (82)

Paracoccus denitrificans (11)

1a	Copper-bind-3plyD01	D:17-105
1b	Copper-bind-3plyD02	D:17-105
1c	Copper-bind-3plyD03	D:17-105
1d	Copper-bind-3plyD04	D:17-105

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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).

Asymmetric Unit
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1aac	NATIVE OXDIZED AMICYANIN AT 1.3A STRUCTURE
2gb2	P52G MUTANT OF AMICYANIN IN THE CU(II) STATE.
2ov0	HIGH RESOLUTION (0.75A) NATIVE OXDIZED AMICYANIN STRUCTURE
3ie9	STRUCTURE OF OXIDIZED M98L MUTANT OF AMICYANIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

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Sequence-Structure Mapping

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Exons (0, 0)

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