1YEX - JenaLib

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Title :   STRUCTURAL AND BIOCHEMICAL ANALYSIS OF THE LINK BETWEEN ENZYMATIC ACTIVITY AND OLIGOMERIZATION IN AHPC, A BACTERIAL PEROXIREDOXIN.

Authors :   D. Parsonage, D. S. Youngblood, G. N. Sarma, Z. A. Wood, P. A. Karplus, L.

Date :   28 Dec 04 (Deposition) - 16 Aug 05 (Release) - 09 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

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

Reference :   D. Parsonage, D. S. Youngblood, G. N. Sarma, Z. A. Wood, P. A. Karplus, L. B. Poole
Analysis Of The Link Between Enzymatic Activity And Oligomeric State In Ahpc, A Bacterial Peroxiredoxin.
Biochemistry V. 44 10583 2005
PubMed-ID: 16060667 | Reference-DOI: 10.1021/BI050448I

Molecule 1 - ALKYL HYDROPEROXIDE REDUCTASE SUBUNIT C
	Chains	:	A, B, C, D, E
	EC Number	:	1.11.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	AHPC
	Mutation	:	YES
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Synonym	:	ALKYL HYDROPEROXIDE REDUCTASE PROTEIN C22

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 16)

No.	Name	Count	Type	Full Name
1	SO4	16	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO B:47 , SER B:85 , GLU B:86 , THR B:87	BINDING SITE FOR RESIDUE SO4 B 812
2	AC2	SOFTWARE	PRO B:47 , LEU B:50 , ARG B:119 , HOH B:2064	BINDING SITE FOR RESIDUE SO4 B 802
3	AC3	SOFTWARE	SER D:85 , GLU D:86 , THR D:87	BINDING SITE FOR RESIDUE SO4 D 814
4	AC4	SOFTWARE	PRO C:47 , SER C:85 , GLU C:86 , THR C:87	BINDING SITE FOR RESIDUE SO4 C 813
5	AC5	SOFTWARE	TYR A:38 , CYS A:46 , GLU A:49 , LEU A:50 , ARG A:119 , HOH A:1064	BINDING SITE FOR RESIDUE SO4 A 801
6	AC6	SOFTWARE	TYR C:38 , VAL C:45 , PRO C:47 , GLU C:49 , ARG C:119 , HOH C:3064	BINDING SITE FOR RESIDUE SO4 C 803
7	AC7	SOFTWARE	CYS D:46 , PRO D:47 , GLU D:49 , LEU D:50 , ARG D:119 , ARG D:142	BINDING SITE FOR RESIDUE SO4 D 804
8	AC8	SOFTWARE	TYR E:38 , VAL E:45 , PRO E:47 , GLU E:49 , LEU E:50 , ARG E:119	BINDING SITE FOR RESIDUE SO4 E 805

Asymmetric Unit

No.	Residues
1	A:46	-	B:165
2	A:165	-	B:46
3	C:46	-	D:165

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

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

Asymmetric Unit (1, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	AHPC_SALTY	2-157	5	A:1-156 B:1-156 C:1-156 D:1-156 E:1-156

Biological Unit 1 (1, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	AHPC_SALTY	2-157	10	A:1-156 B:1-156 C:1-156 D:1-156 E:1-156

(no "Exon" information available for 1YEX)

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 AHPC_SALTY | P0A251 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
           AHPC_SALTY     2 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGEVCPA 168
               SCOP domains d1yexa1 A:1-166 Alkyl hydroperoxide reductase AhpC                                                                                                                    - SCOP domains
               CATH domains 1yexA00 A:1-167 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..eeeeee.hhh...eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhhh...eeee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: A:1-156 UniProt: 2-157                                                                                                                  ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yex A   1 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFDHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGEVCPA 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with AHPC_SALTY | P0A251 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     
           AHPC_SALTY     2 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGEVC 166
               SCOP domains d1yexb_ B: Alkyl hydroperoxide reductase AhpC                                                                                                                         SCOP domains
               CATH domains 1yexB00 B:1-165 Glutaredoxin                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..eeeeee.hhhh..eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhhh...eeee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: B:1-156 UniProt: 2-157                                                                                                                  --------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yex B   1 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFDHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGEVC 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:163
 aligned with AHPC_SALTY | P0A251 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   
           AHPC_SALTY     2 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGE 164
               SCOP domains d1yexc_ C: Alkyl hydroperoxide reductase AhpC                                                                                                                       SCOP domains
               CATH domains 1yexC00 C:1-163 Glutaredoxin                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..eeeeee.hhh...eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhh........eeee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: C:1-156 UniProt: 2-157                                                                                                                  ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yex C   1 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFDHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGE 163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain D from PDB  Type:PROTEIN  Length:166
 aligned with AHPC_SALTY | P0A251 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:166
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      
           AHPC_SALTY     2 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGEVCP 167
               SCOP domains d1yexd_ D: Alkyl hydroperoxide reductase AhpC                                                                                                                          SCOP domains
               CATH domains 1yexD00 D:1-166 Glutaredoxin                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..eeeeeehhhhh..eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhh...eeee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: D:1-156 UniProt: 2-157                                                                                                                  ---------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yex D   1 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFDHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGEVCP 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain E from PDB  Type:PROTEIN  Length:165
 aligned with AHPC_SALTY | P0A251 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     
           AHPC_SALTY     2 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGEVC 166
               SCOP domains d1yexe_ E: Alkyl hydroperoxide reductase AhpC                                                                                                                         SCOP domains
               CATH domains 1yexE00 E:1-165 Glutaredoxin                                                                                                                                          CATH domains
           Pfam domains (1) --AhpC-TSA-1yexE01 E:3-133                                                                                                           -------------------1-cysPrx_C-1y Pfam domains (1)
           Pfam domains (2) --AhpC-TSA-1yexE02 E:3-133                                                                                                           -------------------1-cysPrx_C-1y Pfam domains (2)
           Pfam domains (3) --AhpC-TSA-1yexE03 E:3-133                                                                                                           -------------------1-cysPrx_C-1y Pfam domains (3)
           Pfam domains (4) --AhpC-TSA-1yexE04 E:3-133                                                                                                           -------------------1-cysPrx_C-1y Pfam domains (4)
           Pfam domains (5) --AhpC-TSA-1yexE05 E:3-133                                                                                                           -------------------1-cysPrx_C-1y Pfam domains (5)
         Sec.struct. author ..........eeeeee..eeeeee.hhh...eeeeee.........hhhhhhhhhhhhhhhhhheeeeeee..hhhhhhhhh..hhhhhh...eeee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: E:1-156 UniProt: 2-157                                                                                                                  --------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yex E   1 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFDHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPGEVC 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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: Alkyl hydroperoxide reductase AhpC (9)

Salmonella typhimurium [TaxId: 90371] (5)

1a	d1yexa1	A:1-166
1b	d1yexb_	B:
1c	d1yexc_	C:
1d	d1yexd_	D:
1e	d1yexe_	E:

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)

Salmonella typhimurium. Organism_taxid: 602. (6)

1a	1yexC00	C:1-163
1b	1yexB00	B:1-165
1c	1yexE00	E:1-165
1d	1yexD00	D:1-166
1e	1yexA00	A:1-167

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: AhpC-TSA (28)

Salmonella typhimurium (5)

1a	AhpC-TSA-1yexE01	E:3-133
1b	AhpC-TSA-1yexE02	E:3-133
1c	AhpC-TSA-1yexE03	E:3-133
1d	AhpC-TSA-1yexE04	E:3-133
1e	AhpC-TSA-1yexE05	E:3-133

Clan: no clan defined [family: 1-cysPrx_C] (19)

Family: 1-cysPrx_C (19)

Salmonella typhimurium (5)

2a	1-cysPrx_C-1yexE06	E:153-165
2b	1-cysPrx_C-1yexE07	E:153-165
2c	1-cysPrx_C-1yexE08	E:153-165
2d	1-cysPrx_C-1yexE09	E:153-165
2e	1-cysPrx_C-1yexE10	E:153-165

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (AHPC_SALTY | P0A251)

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:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
	GO:0051920	peroxiredoxin activity	Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
biological process
	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.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (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.

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	AHPC_SALTY \| P0A251	:	1n8j 1yep 1yf0 1yf1 3emp 4ma9 4mab 4xra 4xrd 4xs1 4xs4 4xs6 4xs8 4xts

1kyg	SAME PROTEIN WITHOUT MUTATION.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

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