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Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF A PROBABLE THIOL PEROXIDASE FROM STREPTOCOCCUS PNEUMONIAE

Authors :   R. Kniewel, J. Buglino, V. Solorzano, J. Wu, C. D. Lima, S. K. Burley, New Research Center For Structural Genomics (Nysgxrc)

Date :   21 Jun 03 (Deposition) - 08 Jul 03 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B

Keywords :   Structural Genomics, Thiol, Peroxidase, Nysgxrc, T817, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Kniewel, J. Buglino, V. Solorzano, J. Wu, C. D. Lima
Structure Of A Probable Thiol Peroxidase From Streptococcus Pneumoniae
To Be Published
PubMed: search

Molecule 1 - PROBABLE THIOL PEROXIDASE
	Chains	:	A, B
	EC Number	:	1.11.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET T7
	Expression System Strain	:	B834 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TPX
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1PSQ)

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

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

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	TPX_STRP2	16-162	2	A:16-162 B:16-162
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	TPX_STRPN	16-162	2	A:16-162 B:16-162
2	TPX	PS01265	Tpx family signature.	TPX_STRP2	81-92	2	A:81-92 B:81-92
2	TPX	PS01265	Tpx family signature.	TPX_STRPN	81-92	2	A:81-92 B:81-92

(no "Exon" information available for 1PSQ)

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:163
 aligned with TPX_STRP2 | Q04JB8 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
            TPX_STRP2     1 MVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSMDLPFAQKRWCGAEGLDNAIMLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
               SCOP domains d1psqa_ A: Probable thiol peroxidase PsaD                                                                                                                           SCOP domains
               CATH domains -1psqA00 A:2-163 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................eee.....eee.hhhh..eeeeee.....hhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhh....eeee....hhhhhhh............eeeee.....eeeeee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------THIOREDOXIN_2  PDB: A:16-162 UniProt: 16-162                                                                                                       - PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------TPX         ----------------------------------------------------------------------- PROSITE (4)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1psq A   1 mVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSmDLPFAQKRWCGAEGLDNAImLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
                            |       10        20        30        40        50        60        70        80 |      90       100 |     110       120       130       140       150       160   
                            |                                                                               82-MSE             102-MSE                                                         
                            1-MSE

Chain A from PDB  Type:PROTEIN  Length:163
 aligned with TPX_STRPN | P0C2J8 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
            TPX_STRPN     1 MVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSMDLPFAQKRWCGAEGLDNAIMLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
               SCOP domains d1psqa_ A: Probable thiol peroxidase PsaD                                                                                                                           SCOP domains
               CATH domains -1psqA00 A:2-163 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................eee.....eee.hhhh..eeeeee.....hhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhh....eeee....hhhhhhh............eeeee.....eeeeee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------THIOREDOXIN_2  PDB: A:16-162 UniProt: 16-162                                                                                                       - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------TPX         ----------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1psq A   1 mVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSmDLPFAQKRWCGAEGLDNAImLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
                            |       10        20        30        40        50        60        70        80 |      90       100 |     110       120       130       140       150       160   
                            1-MSE                                                                           82-MSE             102-MSE

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with TPX_STRP2 | Q04JB8 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
            TPX_STRP2     1 MVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSMDLPFAQKRWCGAEGLDNAIMLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
               SCOP domains d1psqb_ B: Probable thiol peroxidase PsaD                                                                                                                           SCOP domains
               CATH domains -1psqB00 B:2-163 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee.................eee....eehhhhhh..eeeeee.....hhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhh....eeee....hhhhhhh............eeeee.....eeeeee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------THIOREDOXIN_2  PDB: B:16-162 UniProt: 16-162                                                                                                       - PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------TPX         ----------------------------------------------------------------------- PROSITE (4)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1psq B   1 mVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSmDLPFAQKRWCGAEGLDNAImLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
                            |       10        20        30        40        50        60        70        80 |      90       100 |     110       120       130       140       150       160   
                            1-MSE                                                                           82-MSE             102-MSE

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with TPX_STRPN | P0C2J8 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
            TPX_STRPN     1 MVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSMDLPFAQKRWCGAEGLDNAIMLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
               SCOP domains d1psqb_ B: Probable thiol peroxidase PsaD                                                                                                                           SCOP domains
               CATH domains -1psqB00 B:2-163 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee.................eee....eehhhhhh..eeeeee.....hhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhh....eeee....hhhhhhh............eeeee.....eeeeee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------THIOREDOXIN_2  PDB: B:16-162 UniProt: 16-162                                                                                                       - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------TPX         ----------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1psq B   1 mVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSmDLPFAQKRWCGAEGLDNAImLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
                            |       10        20        30        40        50        60        70        80 |      90       100 |     110       120       130       140       150       160   
                            1-MSE                                                                           82-MSE             102-MSE

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/Biological 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: Probable thiol peroxidase PsaD (1)

Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313] (1)

1a	d1psqa_	A:
1b	d1psqb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Streptococcus pneumoniae. Organism_taxid: 1313. (1)

1a	1psqA00	A:2-163
1b	1psqB00	B:2-163

(no "Pfam Domain" information available for 1PSQ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TPX_STRP2 | Q04JB8)

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: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: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: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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Chain A,B (TPX_STRPN | P0C2J8)

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: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: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: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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Asymmetric/Biological Unit
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