4GQF - JenaLib

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Title :   AEROPYRUM PERNIX PEROXIREDOXIN Q ENZYME IN THE LOCALLY UNFOLDED CONFORMATION

Authors :   A. Perkins, P. A. Karplus, M. C. Gretes, K. J. Nelson, L. B. Poole

Date :   22 Aug 12 (Deposition) - 24 Oct 12 (Release) - 20 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Peroxiredoxin, Dimer, Prxq, Bcp, Locally-Unfolded, Cxxxxc, Reduces Peroxides, Disulfide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Perkins, M. C. Gretes, K. J. Nelson, L. B. Poole, P. A. Karplus
Mapping The Active Site Helix-To-Strand Conversion Of Cxxxx Peroxiredoxin Q Enzymes.
Biochemistry V. 51 7638 2012
PubMed-ID: 22928725 | Reference-DOI: 10.1021/BI301017S

Molecule 1 - THIOL PEROXIDASE
	Chains	:	A, B
	EC Number	:	1.11.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	APE2125, APE_2125.1, BCP
	Organism Scientific	:	AEROPYRUM PERNIX
	Organism Taxid	:	272557
	Strain	:	ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
	Synonym	:	PEROXIREDOXIN Q

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A
Biological Unit 2 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 18)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:43 , PHE A:45 , SER A:46 , ASP A:58 , PHE A:84 , ARG A:122 , HOH A:1020 , HOH A:1033	BINDING SITE FOR RESIDUE GOL A 201
02	AC2	SOFTWARE	HIS A:110 , GLU A:111 , ASP A:112	BINDING SITE FOR RESIDUE SO4 A 202
03	AC3	SOFTWARE	GLN A:62 , LYS A:65 , ARG B:89	BINDING SITE FOR RESIDUE SO4 A 203
04	AC4	SOFTWARE	ARG A:57 , LYS A:59	BINDING SITE FOR RESIDUE SO4 A 204
05	AC5	SOFTWARE	ALA B:43 , PHE B:45 , SER B:46 , ASP B:58 , MSE B:60 , PHE B:84 , ARG B:122 , HOH B:319 , HOH B:320	BINDING SITE FOR RESIDUE GOL B 201
06	AC6	SOFTWARE	HIS B:110 , GLU B:111 , ASP B:112	BINDING SITE FOR RESIDUE SO4 B 202
07	AC7	SOFTWARE	ARG A:89 , GLN B:62 , LYS B:65 , HOH B:310	BINDING SITE FOR RESIDUE SO4 B 203
08	AC8	SOFTWARE	ARG B:57 , LYS B:59 , HOH B:310	BINDING SITE FOR RESIDUE SO4 B 204
09	AC9	SOFTWARE	TYR B:135 , TRP B:137 , ASP B:147 , GLU B:150 , VAL B:151	BINDING SITE FOR RESIDUE SO4 B 205
10	BC1	SOFTWARE	TRP B:137 , VAL B:138	BINDING SITE FOR RESIDUE SO4 B 206
11	BC2	SOFTWARE	GLU B:150 , ARG B:153 , GLU B:154	BINDING SITE FOR RESIDUE SO4 B 207

Asymmetric Unit

No.	Residues
1	A:49	-	A:54
2	B:49	-	B:54

(no "Cis Peptide Bond" information available for 4GQF)

(no "SAP(SNP)/Variant" information available for 4GQF)

(no "PROSITE Motif" information available for 4GQF)

(no "Exon" information available for 4GQF)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:163
                                                                                                                                                                                                   
               SCOP domains d4gqfa_ A: Bacterioferritin comigratory protein                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee.....eeehhhhhh....eeeee.......ee....ee...hhhhhhhh..eeeeee..hhhhhhhhhhhh....eeee...hhhhhhhh.eeeee..eeeee..eeeee.....eeeeee........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gqf A   2 KGLVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKmAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKmVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELVA 164
                                    11        21        31        41        51        61        71        81        91       101       111      |121       131       141       151       161   
                                                                                     60-MSE                                                   118-MSE

Chain B from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains d4gqfb_ B: Bacterioferritin comigratory protein                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eee.....eeehhhhhh....eeeee.......ee....ee...hhhhhhhh..eeeeee..hhhhhhhhhhhh....eeee...hhhhhhh..eeeee..eeeee.eeeeee.....eeeeeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gqf B   3 GLVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKmAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKmVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELVA 164
                                    12        22        32        42        52       |62        72        82        92       102       112     | 122       132       142       152       162  
                                                                                    60-MSE                                                   118-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: Glutathione peroxidase-like (136)

Protein domain: Bacterioferritin comigratory protein (4)

Aeropyrum pernix [TaxId: 56636] (4)

1a	d4gqfa_	A:
1b	d4gqfb_	B:

(no "CATH Domain" information available for 4GQF)

(no "Pfam Domain" information available for 4GQF)

Asymmetric Unit(hide GO term definitions)

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	Q9YA14_AERPE \| Q9YA14	:	2cx3 2cx4 4gqc

2cx3	CRYSTAL STRUCTURE OF A BACTERIOFERRITIN COMIGRATORY PROTEIN PEROXIREDOXIN FROM THE AEROPYRUM PERNIX K1 (FORM-1 CRYSTAL) . THIS ENTRY 4GQF REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R2CX3SF.
2cx4	CRYSTAL STRUCTURE OF A BACTERIOFERRITIN COMIGRATORY PROTEIN PEROXIREDOXIN FROM THE AEROPYRUM PERNIX K1 (FORM-2 CRYSTAL)
2g2e
2gqc
2ywn	CRYSTAL STRUCTURE OF PEROXIREDOXIN-LIKE PROTEIN FROM SULFOLOBUS TOKODAII.

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (11, 11)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (5, 5)

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