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(-) Description

Title :  CRYSTAL STRUCTURE OF AEROPYRUM PERNIX PEROXIREDOXIN Q ENZYME IN FULLY-FOLDED AND LOCALLY-UNFOLDED CONFORMATIONS
 
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 :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Cxxxxc Motif, Fully Folded, Locally Unfolded, Peroxide, Dtt, Structural Genomics, Riken, Peroxiredoxin, 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

(-) Compounds

Molecule 1 - THIOL PEROXIDASE
    Chains: A, B, C, D
    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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 36)

Asymmetric Unit (3, 36)
No.NameCountTypeFull Name
1DTD2Ligand/IonDITHIANE DIOL
2GOL3Ligand/IonGLYCEROL
3SO431Ligand/IonSULFATE ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1DTD1Ligand/IonDITHIANE DIOL
2GOL1Ligand/IonGLYCEROL
3SO416Ligand/IonSULFATE ION
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
1DTD1Ligand/IonDITHIANE DIOL
2GOL2Ligand/IonGLYCEROL
3SO415Ligand/IonSULFATE ION

(-) Sites  (36, 36)

Asymmetric Unit (36, 36)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:137 , ASN A:144 , SO4 A:207BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWAREARG A:32 , GLU A:69 , ASN A:93 , HOH A:324BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWAREHIS A:110 , GLU A:111 , ASP A:112BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWARETHR A:50 , LYS A:51 , HOH D:356BINDING SITE FOR RESIDUE SO4 A 204
05AC5SOFTWAREARG A:34 , ALA A:68BINDING SITE FOR RESIDUE SO4 A 205
06AC6SOFTWAREARG A:57 , LYS D:157BINDING SITE FOR RESIDUE SO4 A 206
07AC7SOFTWAREVAL A:138 , THR A:139 , ASP A:140 , SO4 A:201BINDING SITE FOR RESIDUE SO4 A 207
08AC8SOFTWAREVAL A:24 , ASN A:25 , GLU A:28 , VAL A:29 , ARG A:32 , HOH A:325BINDING SITE FOR RESIDUE SO4 A 208
09AC9SOFTWAREPHE A:14 , THR A:15 , GLU A:101BINDING SITE FOR RESIDUE SO4 A 209
10BC1SOFTWARETHR A:50 , LYS A:51 , GLU A:52 , CYS A:54 , LYS D:136 , VAL D:138 , SO4 D:204BINDING SITE FOR RESIDUE SO4 A 210
11BC2SOFTWAREGLU B:22 , PRO B:23 , VAL B:24 , ASN B:25 , GLU B:28 , VAL B:29 , ARG B:32BINDING SITE FOR RESIDUE GOL B 201
12BC3SOFTWAREVAL B:75 , TYR B:98 , ARG B:100 , HOH B:1011 , VAL D:75 , TYR D:98 , ARG D:100BINDING SITE FOR RESIDUE GOL B 202
13BC4SOFTWARETRP B:137 , ASN B:144 , SO4 B:205 , HOH B:1029BINDING SITE FOR RESIDUE SO4 B 203
14BC5SOFTWAREHIS B:110 , GLU B:111 , ASP B:112BINDING SITE FOR RESIDUE SO4 B 204
15BC6SOFTWARETHR B:139 , ASP B:140 , ASN B:141 , SO4 B:203BINDING SITE FOR RESIDUE SO4 B 205
16BC7SOFTWARETHR B:50 , LYS B:51 , HOH B:1087BINDING SITE FOR RESIDUE SO4 B 206
17BC8SOFTWAREARG B:34BINDING SITE FOR RESIDUE SO4 B 207
18BC9SOFTWAREPRO B:47 , LYS B:114 , LEU B:143 , SO4 B:210 , HOH B:1062 , GLU C:6 , HOH C:361 , TRP D:79BINDING SITE FOR RESIDUE SO4 B 208
19CC1SOFTWAREASP B:13 , PHE B:14 , THR B:15 , ASN B:25 , HOH B:1002 , HOH B:1059BINDING SITE FOR RESIDUE SO4 B 209
20CC2SOFTWARELYS B:114 , SO4 B:208 , GLU C:6 , LEU C:7 , GLU C:9 , ASP D:20 , PHE D:21BINDING SITE FOR RESIDUE SO4 B 210
21CC3SOFTWAREVAL A:75 , TYR A:98 , ARG A:100 , HOH A:310 , VAL C:75 , TYR C:98 , ARG C:100 , HOH C:320BINDING SITE FOR RESIDUE GOL C 201
22CC4SOFTWARETRP A:79 , SER C:46 , PRO C:47 , VAL C:48 , CYS C:49 , LEU C:113 , ARG C:122 , PRO C:142 , HOH C:369BINDING SITE FOR RESIDUE DTD C 202
23CC5SOFTWAREHIS C:110 , GLU C:111 , ASP C:112 , HOH C:347BINDING SITE FOR RESIDUE SO4 C 203
24CC6SOFTWAREGLU B:52 , ASN C:141 , ASN C:144 , HOH C:325BINDING SITE FOR RESIDUE SO4 C 204
25CC7SOFTWARELYS C:104 , MET C:118BINDING SITE FOR RESIDUE SO4 C 205
26CC8SOFTWARETHR B:50 , LYS B:51 , GLU B:52 , CYS B:54 , LYS C:136 , VAL C:138 , HOH C:313BINDING SITE FOR RESIDUE SO4 C 206
27CC9SOFTWARELYS B:31 , ASN C:144 , GLU C:145BINDING SITE FOR RESIDUE SO4 C 207
28DC1SOFTWARELYS C:51BINDING SITE FOR RESIDUE SO4 C 208
29DC2SOFTWARETRP B:79 , SER D:46 , PRO D:47 , VAL D:48 , CYS D:49 , LEU D:113 , ARG D:122 , HOH D:327BINDING SITE FOR RESIDUE DTD D 201
30DC3SOFTWAREHIS D:110 , GLU D:111 , ASP D:112 , HOH D:341BINDING SITE FOR RESIDUE SO4 D 202
31DC4SOFTWARELYS A:31 , ASN D:144 , GLU D:145BINDING SITE FOR RESIDUE SO4 D 203
32DC5SOFTWARESO4 A:210 , LEU D:4 , ASN D:107 , LYS D:136BINDING SITE FOR RESIDUE SO4 D 204
33DC6SOFTWAREARG D:57 , GLN D:62 , ARG D:89 , HOH D:343BINDING SITE FOR RESIDUE SO4 D 205
34DC7SOFTWAREARG C:32 , ARG D:32BINDING SITE FOR RESIDUE SO4 D 206
35DC8SOFTWAREARG D:100 , LYS D:104 , MET D:118 , HOH D:361BINDING SITE FOR RESIDUE SO4 D 207
36DC9SOFTWARELYS A:31 , ARG A:32 , LYS D:51BINDING SITE FOR RESIDUE SO4 D 208

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GQC)

(-) Sequences/Alignments

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:160
                                                                                                                                                                                                
               SCOP domains d4gqca_ A: Bacterioferritin comigratory protein                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee.....eeehhhhhhh...eeeee.......ee....ee...hhhhhhhh..eeeeee..hhhhhhhhhhhh....eeee...hhhhhhh..eeeee..eeeee..eeeee.....eeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gqc A   4 LVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKMAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKMVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 163
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163


Chain B from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains d4gqcb_ B: Bacterioferritin comigratory protein                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee.....eeehhhhhhh...eeeee.......ee....ee...hhhhhhhh..eeeeee..hhhhhhhhhhhh....eeee...hhhhhhh..eeeee..eeeee..eeeee.....eeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gqc B   4 LVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKMAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKMVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 163
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163


Chain C from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains d4gqcc_ C: Bacterioferritin comigratory protein                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee.....eeehhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh...eeee...hhhhhhh..eeeee..eeeee..eeeee.....eeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gqc C   3 GLVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKMAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKMVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 163
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 


Chain D from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains d4gqcd_ D: Bacterioferritin comigratory protein                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee.....eeehhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh...eeee...hhhhhhh..eeeee..eeeee..eeeee.....eeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gqc D   3 GLVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKMAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKMVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 163
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        Q9YA14_AERPE | Q9YA14: 2cx3 2cx4 4gqf

(-) Related Entries Specified in the PDB File

2cx3 CRYSTAL STRUCTURE OF A BACTERIOFERRITIN COMIGRATORY PROTEIN PEROXIREDOXIN FROM THE AEROPYRUM PERNIX K1 (FORM-1 CRYSTAL).
2cx4 CRYSTAL STRUCTURE OF A BACTERIOFERRITIN COMIGRATORY PROTEIN PEROXIREDOXIN FROM THE AEROPYRUM PERNIX K1 (FORM-2 CRYSTAL) . THIS ENTRY 4GQC REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R2CX4SF.
2g2e
2gqf
2ywn CRYSTAL STRUCTURE OF PEROXIREDOXIN-LIKE PROTEIN FROM SULFOLOBUS TOKODAII.