1Q98 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF A THIOL PEROXIDASE FROM HAEMOPHILUS INFLUENZAE RD

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

Date :   22 Aug 03 (Deposition) - 09 Sep 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Structural Genomics, Tpx, Peroxidase, Nysgxrc, T1429, 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 Thiol Peroxidase From Haemophilus Influenzae Rd
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - THIOL PEROXIDASE
	Chains	:	A, B
	EC Number	:	1.11.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET T7
	Gene	:	TPX, HI0751
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	TPX

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1Q98)

(no "Site" information available for 1Q98)

Asymmetric/Biological Unit

No.	Residues
1	A:59	-	A:93
2	B:59	-	B:93

(no "Cis Peptide Bond" information available for 1Q98)

(no "SAP(SNP)/Variant" information available for 1Q98)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	TPX_HAEIN	17-165	2	A:17-165 B:17-165
2	TPX	PS01265	Tpx family signature.	TPX_HAEIN	82-93	2	A:82-93 B:82-93

(no "Exon" information available for 1Q98)

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
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Chain A from PDB  Type:PROTEIN  Length:164
 aligned with TPX_HAEIN | Q57549 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            TPX_HAEIN     2 TVTLAGNPIEVGGHFPQVGEIVENFILVGNDLADVALNDFASKRKVLNIFPSIDTGVCATSVRKFNQQAAKLSNTIVLCISADLPFAQARFCGAEGIENAKTVSTFRNHALHSQLGVDIQTGPLAGLTSRAVIVLDEQNNVLHSQLVEEIKEEPNYEAALAVLA 165
               SCOP domains d1q98a_ A: Thiol peroxidase Tpx                                                                                                                                      SCOP domains
               CATH domains 1q98A00 A:2-165 Glutaredoxin                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee.ee.............eee.....eee.hhhh..eeeeee.........hhhhhhhhhhhhhh..eeeeeee..hhhhhh..........eeeee....hhhhhhh..ee...........eeeee.....eeeeee........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------THIOREDOXIN_2  PDB: A:17-165 UniProt: 17-165                                                                                                          PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q98 A   2 TVTLAGNPIEVGGHFPQVGEIVENFILVGNDLADVALNDFASKRKVLNIFPSIDTGVCATSVRKFNQQAAKLSNTIVLCISADLPFAQARFCGAEGIENAKTVSTFRNHALHSQLGVDIQTGPLAGLTSRAVIVLDEQNNVLHSQLVEEIKEEPNYEAALAVLA 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with TPX_HAEIN | Q57549 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            TPX_HAEIN     2 TVTLAGNPIEVGGHFPQVGEIVENFILVGNDLADVALNDFASKRKVLNIFPSIDTGVCATSVRKFNQQAAKLSNTIVLCISADLPFAQARFCGAEGIENAKTVSTFRNHALHSQLGVDIQTGPLAGLTSRAVIVLDEQNNVLHSQLVEEIKEEPNYEAALAVLA 165
               SCOP domains d1q98b_ B: Thiol peroxidase Tpx                                                                                                                                      SCOP domains
               CATH domains 1q98B00 B:2-165 Glutaredoxin                                                                                                                                         CATH domains
           Pfam domains (1) ---------Redoxin-1q98B01 B:11-161                                                                                                                               ---- Pfam domains (1)
           Pfam domains (2) ---------Redoxin-1q98B02 B:11-161                                                                                                                               ---- Pfam domains (2)
         Sec.struct. author .eee..eee.ee.............eee.....eee.hhhh..eeeeee..........hhhhhhhhhhhh...eeeeeee..hhhhhh..........eeeee....hhhhhhh..ee...........eeeee.....eeeeee........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------THIOREDOXIN_2  PDB: B:17-165 UniProt: 17-165                                                                                                          PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q98 B   2 TVTLAGNPIEVGGHFPQVGEIVENFILVGNDLADVALNDFASKRKVLNIFPSIDTGVCATSVRKFNQQAAKLSNTIVLCISADLPFAQARFCGAEGIENAKTVSTFRNHALHSQLGVDIQTGPLAGLTSRAVIVLDEQNNVLHSQLVEEIKEEPNYEAALAVLA 165
                                    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/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: Thiol peroxidase Tpx (8)

Haemophilus influenzae [TaxId: 727] (1)

1a	d1q98a_	A:
1b	d1q98b_	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)

Haemophilus influenzae. Organism_taxid: 727. (2)

1a	1q98A00	A:2-165
1b	1q98B00	B:2-165

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: Redoxin (27)

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (2)

1a	Redoxin-1q98B01	B:11-161
1b	Redoxin-1q98B02	B:11-161

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TPX_HAEIN | Q57549)

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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	1q98
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Description

Compounds

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

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