3HVX - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ESCHERICHIA COLI THIOL PEROXIDASE (TPX) RESOLVING CYSTEINE TO SERINE MUTANT (C95S) WITH AN INTERMOLECULAR DISULFIDE BOND

Authors :   A. Hall, B. Sankaran, P. A. Karplus

Date :   16 Jun 09 (Deposition) - 20 Oct 09 (Release) - 03 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.12

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

Keywords :   Oxidoreductase, Tpx, Peroxiredoxin, Peroxidase, Antioxidant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Hall, B. Sankaran, L. B. Poole, P. A. Karplus
Structural Changes Common To Catalysis In The Tpx Peroxiredoxin Subfamily.
J. Mol. Biol. V. 393 867 2009
PubMed-ID: 19699750 | Reference-DOI: 10.1016/J.JMB.2009.08.040
(for further references see the PDB file header)

Molecule 1 - THIOL PEROXIDASE
	Chains	:	A, B, C, D
	EC Number	:	1.11.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROK1
	Expression System Strain	:	XL-1 BLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B1324, JW1317, TPX, YZZJ
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	K-12 (XL-1 BLUE)
	Synonym	:	SCAVENGASE P20

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 11)

No.	Name	Count	Type	Full Name
1	CL	11	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:27 , PHE A:28 , THR A:39 , LEU A:40 , GLY A:41 , HOH A:213	BINDING SITE FOR RESIDUE CL A 169
02	AC2	SOFTWARE	GLN A:148 , ASP A:151	BINDING SITE FOR RESIDUE CL A 170
03	AC3	SOFTWARE	GLN B:148 , LEU B:149 , ASP B:151	BINDING SITE FOR RESIDUE CL B 169
04	AC4	SOFTWARE	THR B:27 , LEU B:40 , GLY B:41	BINDING SITE FOR RESIDUE CL B 170
05	AC5	SOFTWARE	ARG B:133 , HOH B:336	BINDING SITE FOR RESIDUE CL B 171
06	AC6	SOFTWARE	THR C:27 , LEU C:40 , GLY C:41	BINDING SITE FOR RESIDUE CL C 1
07	AC7	SOFTWARE	ARG C:133 , GLU C:156 , HOH C:593	BINDING SITE FOR RESIDUE CL C 169
08	AC8	SOFTWARE	GLN C:148 , ASP C:151	BINDING SITE FOR RESIDUE CL C 170
09	AC9	SOFTWARE	THR D:27 , PHE D:28 , THR D:39 , LEU D:40 , GLY D:41	BINDING SITE FOR RESIDUE CL D 169
10	BC1	SOFTWARE	GLN D:8 , GLU D:152 , ILE D:153 , THR D:154	BINDING SITE FOR RESIDUE CL D 170
11	BC2	SOFTWARE	GLN D:148 , ASP D:151	BINDING SITE FOR RESIDUE CL D 171

Asymmetric Unit

No.	Residues
1	A:61	-	B:61
2	C:61	-	D:61

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

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	TPX_ECOLI	19-168	4	A:19-168 B:19-168 C:19-168 D:19-168
2	TPX	PS01265	Tpx family signature.	TPX_ECOLI	84-95	4	A:84-94 B:84-94 C:84-94 D:84-94

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	TPX_ECOLI	19-168	2	A:19-168 - C:19-168 -
2	TPX	PS01265	Tpx family signature.	TPX_ECOLI	84-95	2	A:84-94 - C:84-94 -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	TPX_ECOLI	19-168	2	- B:19-168 - D:19-168
2	TPX	PS01265	Tpx family signature.	TPX_ECOLI	84-95	2	- B:84-94 - D:84-94

(no "Exon" information available for 3HVX)

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:167
 aligned with TPX_ECOLI | P0A862 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
            TPX_ECOLI     2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLCISADLPFAQSRFCGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
               SCOP domains d3hvxa_ A: Thiol peroxidase Tpx                                                                                                                                         SCOP domains
               CATH domains 3hvxA00 A:2-168 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee..............eee.....eee.hhhh..eeeeee........hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh......eeeee....hhhhhhh.....hhhhh.....eeeee.....eeeeee........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------THIOREDOXIN_2  PDB: A:19-168 UniProt: 19-168                                                                                                           PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hvx A   2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLSISADLPFAQSRFSGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:167
 aligned with TPX_ECOLI | P0A862 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
            TPX_ECOLI     2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLCISADLPFAQSRFCGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
               SCOP domains d3hvxb_ B: Thiol peroxidase Tpx                                                                                                                                         SCOP domains
               CATH domains 3hvxB00 B:2-168 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee..............eee.....eee.hhhh..eeeeeee.......hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhh......eeeee....hhhhhhh...............eeeee.....eeeeee........hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------THIOREDOXIN_2  PDB: B:19-168 UniProt: 19-168                                                                                                           PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hvx B   2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLSISADLPFAQSRFSGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain C from PDB  Type:PROTEIN  Length:167
 aligned with TPX_ECOLI | P0A862 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
            TPX_ECOLI     2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLCISADLPFAQSRFCGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
               SCOP domains d3hvxc_ C: Thiol peroxidase Tpx                                                                                                                                         SCOP domains
               CATH domains 3hvxC00 C:2-168 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee..............eee.....eee.hhhh..eeeeeee.......hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhh......eeeee....hhhhhhh...............eeeee.....eeeeee........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------THIOREDOXIN_2  PDB: C:19-168 UniProt: 19-168                                                                                                           PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hvx C   2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLSISADLPFAQSRFSGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain D from PDB  Type:PROTEIN  Length:167
 aligned with TPX_ECOLI | P0A862 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
            TPX_ECOLI     2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLCISADLPFAQSRFCGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
               SCOP domains d3hvxd_ D: Thiol peroxidase Tpx                                                                                                                                         SCOP domains
               CATH domains 3hvxD00 D:2-168 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee..............eee.....eee.hhhh..eeeeee........hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhh......eeeee....hhhhhhh...............eeeee.....eeeeee........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------THIOREDOXIN_2  PDB: D:19-168 UniProt: 19-168                                                                                                           PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hvx D   2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLSISADLPFAQSRFSGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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: Glutathione peroxidase-like (136)

Protein domain: Thiol peroxidase Tpx (8)

Escherichia coli K-12 [TaxId: 83333] (4)

1a	d3hvxa_	A:
1b	d3hvxb_	B:
1c	d3hvxc_	C:
1d	d3hvxd_	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 k-12. Organism_taxid: 83333. Strain: k-12 (xl-1 blue). (4)

1a	3hvxA00	A:2-168
1b	3hvxB00	B:2-168
1c	3hvxC00	C:2-168
1d	3hvxD00	D:2-168

(no "Pfam Domain" information available for 3HVX)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TPX_ECOLI | P0A862)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0032843	hydroperoxide reductase activity	Catalysis of the reaction: 2 RSH + ROOH = RSSR + ROH + H2O. This reaction is the thiol-dependent conversion of an organic hydroperoxide to the corresponding alcohol.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016684	oxidoreductase activity, acting on peroxide as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which the peroxide group acts as a hydrogen or electron acceptor.
	GO:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
	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:0008379	thioredoxin peroxidase activity	Catalysis of the reaction: thioredoxin + hydrogen peroxide = thioredoxin disulfide + H2O.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	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: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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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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	3hvx
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	1.11.1.15
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UniProtKB/Swiss-Prot
	TPX_ECOLI \| P0A862	:	1qxh 3hvs 3hvv 3i43 4af2

1qxh	E. COLI TPX WILD TYPE DISULFIDE FORM AT 2.2 A RESOLUTION
3hvs	E. COLI TPX WILD TYPE DISULFIDE FORM AT 1.8 A RESOLUTION
3hvv	E. COLI TPX C65S MUTANT AT 1.75 A RESOLUTION
3i43	E. COLI TPX WILD TYPE DISULFIDE FORM AT 2.8 A RESOLUTION USED TO CONFIRM THE PRESENCE OF AN INTACT DISULFIDE IN 3HVS

Description

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Ligands, Modified Residues, Ions (1, 11)

Sites (11, 11)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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