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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF THIOREDOXIN FROM LITOPENAEUS VANNAMEI
 
Authors :  A. A. Campos-Acevedo, R. R. Sotelo-Mundo, E. Rudino-Pinera
Date :  05 Sep 11  (Deposition) - 26 Sep 12  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Campos-Acevedo, K. D. Garcia-Orozco, R. R. Sotelo-Mundo, E. Rudino-Pinera
Expression, Purification, Crystallization And X-Ray Crystallographic Studies Of Different Redox States Of The Active Site Of Thioredoxin 1 From The Whiteleg Shrimp Litopenaeus Vannamei
Acta Crystallogr. , Sect. F V. 69 488 2013
PubMed-ID: 23695560  |  Reference-DOI: 10.1107/S1744309113010622

(-) Compounds

Molecule 1 - THIOREDOXIN
    Chains: A, B
    EC Number: 1.8.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET11A
    Expression System Vector Type: PLASMID
    Organism Common: WHITELEG SHRIMP
    Organism Scientific: LITOPENAEUS VANNAMEI
    Organism Taxid: 6689

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2DTU1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3GOL4Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 26)
No.NameCountTypeFull Name
1ACT14Ligand/IonACETATE ION
2DTU2Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3GOL8Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:48 , GLN B:8 , PHE B:11 , THR B:12 , ILE B:65 , ASP B:68 , ASN B:69BINDING SITE FOR RESIDUE DTU A1106
02AC2SOFTWARESER A:90BINDING SITE FOR RESIDUE ACT A1107
03AC3SOFTWARELYS A:6 , GLU A:61 , ASP A:64 , HOH B:2047BINDING SITE FOR RESIDUE ACT A1108
04AC4SOFTWAREASP A:26 , TYR A:28 , ALA A:39 , LYS A:56 , HOH A:2029 , HOH A:2035BINDING SITE FOR RESIDUE ACT A1109
05AC5SOFTWAREPHE A:11 , ASN A:69 , SER B:48BINDING SITE FOR RESIDUE ACT A1110
06AC6SOFTWARELYS A:41 , GLU A:44 , ASN B:16 , GLY B:83BINDING SITE FOR RESIDUE ACT A1111
07AC7SOFTWAREASN A:16 , ASN A:82 , GLY A:83 , HOH A:2019 , HOH A:2024 , LYS B:41 , GLU B:44 , HOH B:2031BINDING SITE FOR RESIDUE GOL A1112
08AC8SOFTWAREALA A:92 , ASN A:93 , TYR A:94 , ASP A:95 , LYS B:81 , ASN B:82 , GLN B:84BINDING SITE FOR RESIDUE GOL A1113
09AC9SOFTWARELYS A:41 , GLU A:44 , TYR A:94 , ASN B:16 , GLY B:19 , ASN B:82 , HOH B:2015BINDING SITE FOR RESIDUE GOL A1114
10BC1SOFTWAREGLU A:17 , ALA A:18 , LYS A:21 , VAL A:53 , HOH A:2016 , HOH A:2022BINDING SITE FOR RESIDUE GOL A1115
11BC2SOFTWARELYS B:13 , GLU B:17 , GLY B:19 , ASN B:20 , LYS B:21 , HOH B:2011BINDING SITE FOR RESIDUE SO4 B1106
12BC3SOFTWAREASN B:69 , LYS B:85 , SER B:88BINDING SITE FOR RESIDUE ACT B1107
13BC4SOFTWAREASP A:7 , GLN A:8 , GLU A:9 , ASP B:51 , LYS B:105 , HOH B:2047BINDING SITE FOR RESIDUE ACT B1108

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:32 -A:35
2A:73 -B:73
3B:32 -B:35

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Met A:74 -Pro A:75
2Met B:74 -Pro B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZZX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZZX)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZZX)

(-) 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:105
 aligned with B1PWB9_LITVA | B1PWB9 from UniProtKB/TrEMBL  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
         B1PWB9_LITVA     1 MVYQVKDQEDSTKQLNEAGNKLVVIDFYATWCGPCKMIAPKLEELSQSMSDVVFLKVDVDECEDIAQDNQIACMPTFLFMKNGQKLDSLSGANYDKLLELVEKNK 105
               SCOP domains d3zzxa_ A: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3zzx A   1 MVYQVKDQEDFTKQLNEAGNKLVVIDFYATWCGPCKMIAPKLEELSQSMSDVVFLKVDVDECEDIAQDNQIACMPTFLFMKNGQKLDSLSGANYDKLLELVEKNK 105
                                    10        20        30        40        50        60        70        80        90       100     


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with B1PWB9_LITVA | B1PWB9 from UniProtKB/TrEMBL  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
         B1PWB9_LITVA     1 MVYQVKDQEDSTKQLNEAGNKLVVIDFYATWCGPCKMIAPKLEELSQSMSDVVFLKVDVDECEDIAQDNQIACMPTFLFMKNGQKLDSLSGANYDKLLELVEKNK 105
               SCOP domains d3zzxb_ B: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3zzx B   1 MVYQVKDQEDFTKQLNEAGNKLVVIDFYATWCGPCKMIAPKLEELSQSMSDVVFLKVDVDECEDIAQDNQIACMPTFLFMKNGQKLDSLSGANYDKLLELVEKNK 105
                                    10        20        30        40        50        60        70        80        90       100
   Legend:   → Mismatch (orange background)
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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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZZX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZZX)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (B1PWB9_LITVA | B1PWB9)
molecular function
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0006662    glycerol ether metabolic process    The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
    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.

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  3zzx
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 Related Entries

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

UniProtKB/TrEMBL
        B1PWB9_LITVA | B1PWB9: 4aj6 4aj7 4aj8 4v2l 4v2m 4v2n 5g2z 5g30 5g31

(-) Related Entries Specified in the PDB File

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