2V2G - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE C45S MUTANT OF THE PEROXIREDOXIN 6 OF ARENICOLA MARINA. MONOCLINIC FORM

Authors :   A. Smeets, J. P. Declercq

Date :   05 Jun 07 (Deposition) - 08 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Oxidoreductase, Peroxiredoxins, Antioxidant Enzymes, Arenicola Marina (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Smeets, E. Loumaye, A. Clippe, J. F. Rees, B. Knoops, J. P. Declercq
The Crystal Structure Of The C45S Mutant Of Annelid Arenicola Marina Peroxiredoxin 6 Supports Its Assignment To The Mechanistically Typical 2- Cys Subfamily Without Any Formation Of Toroid- Shaped Decamers.
Protein Sci. V. 17 700 2008
PubMed-ID: 18359859 | Reference-DOI: 10.1110/PS.073399308

Molecule 1 - PEROXIREDOXIN 6
	Chains	:	A, B, C, D
	EC Number	:	1.11.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-60
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	LUGWORM
	Organism Scientific	:	ARENICOLA MARINA
	Organism Taxid	:	6344
	Synonym	:	PEROXIREDOXIN 6 OF ARENICOLA MARINA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	BEZ	4	Ligand/Ion	BENZOIC ACID
2	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	BEZ	2	Ligand/Ion	BENZOIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	BEZ	2	Ligand/Ion	BENZOIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:42 , PRO A:43 , VAL A:44 , SER A:45 , GLU A:117 , ARG A:128 , HOH A:2066	BINDING SITE FOR RESIDUE BEZ A1222
2	AC2	SOFTWARE	THR B:42 , PRO B:43 , VAL B:44 , SER B:45 , GLU B:117 , ARG B:128 , HOH B:2080 , HOH B:2190	BINDING SITE FOR RESIDUE BEZ B1220
3	AC3	SOFTWARE	THR C:42 , PRO C:43 , VAL C:44 , SER C:45 , GLU C:117 , ARG C:128 , HOH C:2069	BINDING SITE FOR RESIDUE BEZ C1222
4	AC4	SOFTWARE	THR D:42 , PRO D:43 , VAL D:44 , SER D:45 , GLU D:117 , ARG D:128 , HOH D:2083 , HOH D:2206	BINDING SITE FOR RESIDUE BEZ D1221
5	AC5	SOFTWARE	PRO C:187 , TYR C:212 , HOH C:2231	BINDING SITE FOR RESIDUE GOL C1223
6	AC6	SOFTWARE	THR B:47 , GLY B:50 , ARG B:51 , GLN B:54 , LEU B:87 , HOH B:2253 , HOH B:2254 , HOH B:2255	BINDING SITE FOR RESIDUE GOL B1221
7	AC7	SOFTWARE	PRO A:187 , GLY A:211 , TYR A:212 , HOH A:2251 , HOH A:2252	BINDING SITE FOR RESIDUE GOL A1223
8	AC8	SOFTWARE	ILE C:3 , SER C:142 , LEU C:144 , HOH C:2153 , SER D:142 , LEU D:144 , HOH D:2204	BINDING SITE FOR RESIDUE GOL C1224

(no "SS Bond" information available for 2V2G)

(no "Cis Peptide Bond" information available for 2V2G)

(no "SAP(SNP)/Variant" information available for 2V2G)

(no "PROSITE Motif" information available for 2V2G)

(no "Exon" information available for 2V2G)

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:220
 aligned with Q1AN22_AREMA | Q1AN22 from UniProtKB/TrEMBL  Length:220

    Alignment length:220
                                                                                                                                                                                                                                                    220 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        |-
         Q1AN22_AREMA     2 GITLGEVFPNFEADSTIGKLKFHDWLGNSWGVLFSHPRDFTPVCTTELGRVIQLEGDFKKRGVKLIALSCDNVADHKEWSEDVKCLSGVKGDMPYPIIADETRELAVKLGMVDPDERTSTGMPLTCRAVFIIGPDKKLKLSILYPATTGRNFSEILRVIDSLQLTAQKKVATPADWQPGDRCMVVPGVSAEEAKTLFPNMEVKAVPSGKGYLRYTPQPK-   -
               SCOP domains d2v2ga_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------2v2gA02 A:152-221 Antioxidant, Horf6; Chain A, domain2                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....eehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhh........eee...hhhhhhh..eeeeee.....eee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.ee..........eee....hhhhhhhhh...ee..........eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v2g A   2 GITLGEVFPNFEADSTIGKLKFHDWLGNSWGVLFSHPRDFTPVSTTELGRVIQLEGDFKKRGVKLIALSCDNVADHKEWSEDVKCLSGVKGDMPYPIIADETRELAVKLGMVDPDERTSTGMPLTCRAVFIIGPDKKLKLSILYPATTGRNFSEILRVIDSLQLTAQKKVATPADWQPGDRCMVVPGVSAEEAKTLFPNMEVKAVPSGKGYLRYTPQPKS 221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with Q1AN22_AREMA | Q1AN22 from UniProtKB/TrEMBL  Length:220

    Alignment length:218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        
         Q1AN22_AREMA     2 GITLGEVFPNFEADSTIGKLKFHDWLGNSWGVLFSHPRDFTPVCTTELGRVIQLEGDFKKRGVKLIALSCDNVADHKEWSEDVKCLSGVKGDMPYPIIADETRELAVKLGMVDPDERTSTGMPLTCRAVFIIGPDKKLKLSILYPATTGRNFSEILRVIDSLQLTAQKKVATPADWQPGDRCMVVPGVSAEEAKTLFPNMEVKAVPSGKGYLRYTPQP 219
               SCOP domains d2v2gb_ B: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------2v2gB02 B:152-219 Antioxidant, Horf6; Chain A, domain2               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....eehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhh........eee...hhhhhhh..eeeeee.....eee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.ee..........eee....hhhhhhhhh...ee..........eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v2g B   2 GITLGEVFPNFEADSTIGKLKFHDWLGNSWGVLFSHPRDFTPVSTTELGRVIQLEGDFKKRGVKLIALSCDNVADHKEWSEDVKCLSGVKGDMPYPIIADETRELAVKLGMVDPDERTSTGMPLTCRAVFIIGPDKKLKLSILYPATTGRNFSEILRVIDSLQLTAQKKVATPADWQPGDRCMVVPGVSAEEAKTLFPNMEVKAVPSGKGYLRYTPQP 219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain C from PDB  Type:PROTEIN  Length:220
 aligned with Q1AN22_AREMA | Q1AN22 from UniProtKB/TrEMBL  Length:220

    Alignment length:220
                                                                                                                                                                                                                                                    220 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        |-
         Q1AN22_AREMA     2 GITLGEVFPNFEADSTIGKLKFHDWLGNSWGVLFSHPRDFTPVCTTELGRVIQLEGDFKKRGVKLIALSCDNVADHKEWSEDVKCLSGVKGDMPYPIIADETRELAVKLGMVDPDERTSTGMPLTCRAVFIIGPDKKLKLSILYPATTGRNFSEILRVIDSLQLTAQKKVATPADWQPGDRCMVVPGVSAEEAKTLFPNMEVKAVPSGKGYLRYTPQPK-   -
               SCOP domains d2v2gc_ C: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------2v2gC02 C:152-221 Antioxidant, Horf6; Chain A, domain2                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....eehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhh........eee...hhhhhhh..eeeeee.....eee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhh...ee..........eee....hhhhhhhhh...ee..........eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v2g C   2 GITLGEVFPNFEADSTIGKLKFHDWLGNSWGVLFSHPRDFTPVSTTELGRVIQLEGDFKKRGVKLIALSCDNVADHKEWSEDVKCLSGVKGDMPYPIIADETRELAVKLGMVDPDERTSTGMPLTCRAVFIIGPDKKLKLSILYPATTGRNFSEILRVIDSLQLTAQKKVATPADWQPGDRCMVVPGVSAEEAKTLFPNMEVKAVPSGKGYLRYTPQPKS 221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

Chain D from PDB  Type:PROTEIN  Length:219
 aligned with Q1AN22_AREMA | Q1AN22 from UniProtKB/TrEMBL  Length:220

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
         Q1AN22_AREMA     2 GITLGEVFPNFEADSTIGKLKFHDWLGNSWGVLFSHPRDFTPVCTTELGRVIQLEGDFKKRGVKLIALSCDNVADHKEWSEDVKCLSGVKGDMPYPIIADETRELAVKLGMVDPDERTSTGMPLTCRAVFIIGPDKKLKLSILYPATTGRNFSEILRVIDSLQLTAQKKVATPADWQPGDRCMVVPGVSAEEAKTLFPNMEVKAVPSGKGYLRYTPQPK 220
               SCOP domains d2v2gd_ D: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------2v2gD02 D:152-220 Antioxidant, Horf6; Chain A, domain2                CATH domains
           Pfam domains (1) ---AhpC-TSA-2v2gD01 D:5-142                                                                                                                  -------------------1-cysPrx_C-2v2gD05 D:162-200           -------------------- Pfam domains (1)
           Pfam domains (2) ---AhpC-TSA-2v2gD02 D:5-142                                                                                                                  -------------------1-cysPrx_C-2v2gD06 D:162-200           -------------------- Pfam domains (2)
           Pfam domains (3) ---AhpC-TSA-2v2gD03 D:5-142                                                                                                                  -------------------1-cysPrx_C-2v2gD07 D:162-200           -------------------- Pfam domains (3)
           Pfam domains (4) ---AhpC-TSA-2v2gD04 D:5-142                                                                                                                  -------------------1-cysPrx_C-2v2gD08 D:162-200           -------------------- Pfam domains (4)
         Sec.struct. author ...........eeee....eehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhh........eee...hhhhhhh..eeeeee.....eee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhh...ee..........eee....hhhhhhhhh...ee..........eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v2g D   2 GITLGEVFPNFEADSTIGKLKFHDWLGNSWGVLFSHPRDFTPVSTTELGRVIQLEGDFKKRGVKLIALSCDNVADHKEWSEDVKCLSGVKGDMPYPIIADETRELAVKLGMVDPDERTSTGMPLTCRAVFIIGPDKKLKLSILYPATTGRNFSEILRVIDSLQLTAQKKVATPADWQPGDRCMVVPGVSAEEAKTLFPNMEVKAVPSGKGYLRYTPQPK 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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: automated matches (46)

Arenicola marina [TaxId: 6344] (4)

1a	d2v2ga_	A:
1b	d2v2gb_	B:
1c	d2v2gc_	C:
1d	d2v2gd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Antioxidant, Horf6; Chain A, domain 2 (5)

Homologous Superfamily: Antioxidant, Horf6; Chain A, domain2 (5)

Lugworm (Arenicola marina) (2)

1a	2v2gD02	D:152-220
1b	2v2gA02	A:152-221
1c	2v2gC02	C:152-221
1d	2v2gB02	B:152-219

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: AhpC-TSA (28)

Arenicola marina (Lugworm) (Lumbricus marinus) (3)

1a	AhpC-TSA-2v2gD01	D:5-142
1b	AhpC-TSA-2v2gD02	D:5-142
1c	AhpC-TSA-2v2gD03	D:5-142
1d	AhpC-TSA-2v2gD04	D:5-142

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

Family: 1-cysPrx_C (19)

Arenicola marina (Lugworm) (Lumbricus marinus) (3)

2a	1-cysPrx_C-2v2gD05	D:162-200
2b	1-cysPrx_C-2v2gD06	D:162-200
2c	1-cysPrx_C-2v2gD07	D:162-200
2d	1-cysPrx_C-2v2gD08	D:162-200

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q1AN22_AREMA | Q1AN22)

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: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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2v2g)

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	Q1AN22_AREMA \| Q1AN22	:	2v32 2v41

2v32	CRYSTAL STRUCTURE OF THE C45S MUTANT OF THE PEROXIREDOXIN 6 OF ARENICOLA MARINA. MONOCLINIC FORM 2
2v41	CRYSTAL STRUCTURE OF THE C45S MUTANT OF THE PEROXIREDOXIN 6 OF ARENICOLA MARINA. ORTHORHOMBIC FORM

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