2EIR - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   DESIGN OF DISULFIDE-LINKED THIOREDOXIN DIMERS AND MULTIMERS THROUGH ANALYSIS OF CRYSTAL CONTACTS

Authors :   M. Kobayashi

Date :   13 Mar 07 (Deposition) - 11 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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 :   Thioredoxin, Mutant, Di-Sulfide Bond, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Das, M. Kobayashi, Y. Yamada, S. Sreeramulu, C. Ramakrishnan, S. Wakatsuki, R. Kato, R. Varadarajan
Design Of Disulfide-Linked Thioredoxin Dimers And Multimers Through Analysis Of Crystal Contacts
J. Mol. Biol. V. 372 1278 2007
PubMed-ID: 17727880 | Reference-DOI: 10.1016/J.JMB.2007.07.033

Molecule 1 - THIOREDOXIN 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TRX1, TRX, THIOREDOXIN 12P

		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 (1, 4)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Biological Unit 3 (0, 0)

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

Biological Unit 4 (0, 0)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:1 , ASP A:2	BINDING SITE FOR RESIDUE CU A 201
2	AC2	SOFTWARE	SER B:1 , ASP B:2 , LYS B:3	BINDING SITE FOR RESIDUE CU B 1201
3	AC3	SOFTWARE	SER C:1 , ASP C:2	BINDING SITE FOR RESIDUE CU C 2201
4	AC4	SOFTWARE	SER D:1 , ASP D:2	BINDING SITE FOR RESIDUE CU D 3201

Asymmetric Unit

No.	Residues
1	A:32	-	A:35
2	A:101	-	B:105
3	A:105	-	B:101
4	B:32	-	B:35
5	C:32	-	C:35
6	C:101	-	D:105
7	C:105	-	D:101
8	D:32	-	D:35

Asymmetric Unit

No.	Residues
1	Ile A:75	-	Pro A:76
2	Ile B:75	-	Pro B:76
3	Ile C:75	-	Pro C:76
4	Ile D:75	-	Pro D:76

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO_ECOLI	25-43	4	A:24-42 B:24-42 C:24-42 D:24-42

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO_ECOLI	25-43	1	A:24-42 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO_ECOLI	25-43	1	- B:24-42 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO_ECOLI	25-43	1	- - C:24-42 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO_ECOLI	25-43	1	- - - D:24-42

(no "Exon" information available for 2EIR)

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:107
 aligned with THIO_ECOLI | P0AA25 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:107
                                    11        21        31        41        51        61        71        81        91       101       
           THIO_ECOLI     2 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL 108
               SCOP domains d2eira_ A: automated matches                                                                                SCOP domains
               CATH domains 2eirA00 A:1-107 Glutaredoxin                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhh.....eeeeee..eeeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2eir A   1 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKCFLDCNL 107
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with THIO_ECOLI | P0AA25 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:107
                                    11        21        31        41        51        61        71        81        91       101       
           THIO_ECOLI     2 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL 108
               SCOP domains d2eirb_ B: automated matches                                                                                SCOP domains
               CATH domains 2eirB00 B:1-107 Glutaredoxin                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhhhhh......eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee......hhhhhh.....eeeeee..eeeeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2eir B   1 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKCFLDCNL 107
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:107
 aligned with THIO_ECOLI | P0AA25 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:107
                                    11        21        31        41        51        61        71        81        91       101       
           THIO_ECOLI     2 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL 108
               SCOP domains d2eirc_ C: automated matches                                                                                SCOP domains
               CATH domains 2eirC00 C:1-107 Glutaredoxin                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...............eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeee......hhhhhh.....eeeeee..eeeeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2eir C   1 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKCFLDCNL 107
                                    10        20        30        40        50        60        70        80        90       100

Chain D from PDB  Type:PROTEIN  Length:107
 aligned with THIO_ECOLI | P0AA25 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:107
                                    11        21        31        41        51        61        71        81        91       101       
           THIO_ECOLI     2 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL 108
               SCOP domains d2eird_ D: automated matches                                                                                SCOP domains
               CATH domains 2eirD00 D:1-107 Glutaredoxin                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhh.....eeeeee..eeeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2eir D   1 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKCFLDCNL 107
                                    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: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: Thioltransferase (167)

Protein domain: automated matches (27)

Escherichia coli [TaxId: 562] (1)

1a	d2eira_	A:
1b	d2eirb_	B:
1c	d2eirc_	C:
1d	d2eird_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Escherichia coli. Organism_taxid: 562. (18)

1a	2eirA00	A:1-107
1b	2eirC00	C:1-107
1c	2eirD00	D:1-107
1d	2eirB00	B:1-107

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (THIO_ECOLI | P0AA25)

molecular function
	GO:0016671	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0006662	glycerol ether metabolic process	The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
	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.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0000103	sulfate assimilation	The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
		Ile A:75 - Pro A:76	[ RasMol ]
		Ile B:75 - Pro B:76	[ RasMol ]
		Ile C:75 - Pro C:76	[ RasMol ]
		Ile D:75 - Pro D:76	[ RasMol ]

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	2eir
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2eio	THE SAME PROTEIN(E101C)
2eiq	THE SAME PROTEIN(T89C)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (8, 8)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (11, 11)

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