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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THIOREDOXIN REDUCTASE FROM ENTAMOEBA HISTOLYTICA WITH AUCN
 
Authors :  L. M. Podust
Date :  31 Oct 11  (Deposition) - 07 Nov 12  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Redox Metabolism, Oxidative Stress (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Parsonage, F. Sheng, K. Hirata, A. Debnath, J. H. Mckerrow, S. L. Reed, R. Abagyan, L. B. Poole, L. M. Podust
X-Ray Structures Of Thioredoxin And Thioredoxin Reductase From Entamoeba Histolytica And Prevailing Hypothesis Of The Mechanism Of Auranofin Action.
J. Struct. Biol. V. 194 180 2016
PubMed-ID: 26876147  |  Reference-DOI: 10.1016/J.JSB.2016.02.015

(-) Compounds

Molecule 1 - THIOREDOXIN REDUCTASE
    Chains: A, B
    EC Number: 1.8.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHISA
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector: PTRCHIS
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 5759

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1AU2Ligand/IonGOLD ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
4SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:160 , GLY A:161 , ASP A:162 , ALA A:163 , HIS A:182 , ARG A:183 , ARG A:184 , ARG A:188 , ILE A:246 , HOH A:2199 , HOH A:2231 , HOH A:2232 , HOH A:2242 , HOH A:2252 , HOH A:2298 , HOH A:2370 , HOH A:2371 , ARG B:183 , SO4 B:1316BINDING SITE FOR RESIDUE NDP A1315
2AC2SOFTWAREGLY A:283 , CYS A:286 , HOH A:2347 , HOH A:2374BINDING SITE FOR RESIDUE AU A1316
3AC3SOFTWAREILE A:10 , GLY A:11 , SER A:12 , GLY A:13 , PRO A:14 , ALA A:15 , TYR A:33 , GLU A:34 , GLY A:35 , ALA A:38 , VAL A:41 , ALA A:42 , GLY A:45 , GLN A:46 , LEU A:47 , THR A:50 , ILE A:53 , ASN A:55 , THR A:87 , ILE A:88 , THR A:117 , GLY A:118 , ALA A:119 , HIS A:248 , GLY A:283 , ASP A:284 , ARG A:291 , GLN A:292 , ALA A:293 , ALA A:296 , HOH A:2012 , HOH A:2045 , HOH A:2068 , HOH A:2081 , HOH A:2085 , HOH A:2195 , HOH A:2196 , HOH A:2376 , TYR B:22BINDING SITE FOR RESIDUE FAD A1317
4AC4SOFTWAREMET B:124 , GLY B:160 , GLY B:161 , ALA B:163 , HIS B:182 , ARG B:183 , ARG B:184 , ARG B:188 , ALA B:245 , ILE B:246 , HIS B:248 , ARG B:291 , SO4 B:1316 , HOH B:2160 , HOH B:2189 , HOH B:2191 , HOH B:2205 , HOH B:2216 , HOH B:2217 , HOH B:2270 , HOH B:2332BINDING SITE FOR RESIDUE NDP B1315
5AC5SOFTWAREARG A:183 , NDP A:1315 , HOH A:2199 , ARG B:183 , NDP B:1315BINDING SITE FOR RESIDUE SO4 B1316
6AC6SOFTWAREPRO B:127 , GLY B:128 , GLU B:129 , ASP B:130 , LYS B:131 , HOH B:2162 , HOH B:2333BINDING SITE FOR RESIDUE SO4 B1317
7AC7SOFTWAREGLY B:283 , CYS B:286BINDING SITE FOR RESIDUE AU B1318
8AC8SOFTWARETYR A:22 , HOH A:2022 , HOH A:2028 , ILE B:10 , GLY B:11 , SER B:12 , GLY B:13 , PRO B:14 , ALA B:15 , TYR B:33 , GLU B:34 , GLY B:35 , ALA B:38 , VAL B:41 , ALA B:42 , GLY B:45 , GLN B:46 , LEU B:47 , THR B:50 , ILE B:53 , ASN B:55 , THR B:87 , ILE B:88 , THR B:117 , GLY B:118 , ALA B:119 , GLY B:283 , ASP B:284 , ARG B:291 , GLN B:292 , ALA B:293 , ALA B:296 , HOH B:2012 , HOH B:2036 , HOH B:2052 , HOH B:2061 , HOH B:2149 , HOH B:2150 , HOH B:2274 , HOH B:2336BINDING SITE FOR RESIDUE FAD B1319

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:140 -A:143
2B:140 -B:143

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:96 -Pro A:97
2Gln B:96 -Pro B:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A65)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A65)

(-) Exons   (0, 0)

(no "Exon" information available for 4A65)

(-) Sequences/Alignments

Asymmetric/Biological 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:311
 aligned with C4LW95_ENTHI | C4LW95 from UniProtKB/TrEMBL  Length:314

    Alignment length:311
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313 
         C4LW95_ENTHI     4 IHDVVIIGSGPAAHTAAIYLGRSSLKPVMYEGFMAGGVAAGGQLTTTTIIENFPGFPNGIDGNELMMNMRTQSEKYGTTIITETIDHVDFSTQPFKLFTEEGKEVLTKSVIIATGATAKRMHVPGEDKYWQNGVSACAICDGAVPIFRNKVLMVVGGGDAAMEEALHLTKYGSKVIILHRRDAFRASKTMQERVLNHPKIEVIWNSELVELEGDGDLLNGAKIHNLVSGEYKVVPVAGLFYAIGHSPNSKFLGGQVKTADDGYILTEGPKTSVDGVFACGDVCDRVYRQAIVAAGSGCMAALSCEKWLQTH 314
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh....eee...hhhhh...hhhhhh.ee.........eehhhhhhhhhhhhhhh..eee...eeeee.....eeeee....eeeeeeeee...eee......hhhhhh...ee.hhhhhh.hhhhh..eeeee..hhhhhhhhhhhh....eeeee........hhhhhhhhhh...eeee..eeeeeeee....eeeeeeee.....eeeee..eeee...eee.hhhhh......................eee.hhhh.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a65 A   4 IHDVVIIGSGPAAHTAAIYLGRSSLKPVMYEGFMAGGVAAGGQLTTTTIIENFPGFPNGIDGNELMMNMRTQSEKYGTTIITETIDHVDFSTQPFKLFTEEGKEVLTKSVIIATGATAKRMHVPGEDKYWQNGVSACAICDGAVPIFRNKVLMVVGGGDAAMEEALHLTKYGSKVIILHRRDAFRASKTMQERVLNHPKIEVIWNSELVELEGDGDLLNGAKIHNLVSGEYKVVPVAGLFYAIGHSPNSKFLGGQVKTADDGYILTEGPKTSVDGVFACGDVCDRVYRQAIVAAGSGCMAALSCEKWLQTH 314
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313 


Chain B from PDB  Type:PROTEIN  Length:313
 aligned with C4LW95_ENTHI | C4LW95 from UniProtKB/TrEMBL  Length:314

    Alignment length:313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311   
         C4LW95_ENTHI     2 SNIHDVVIIGSGPAAHTAAIYLGRSSLKPVMYEGFMAGGVAAGGQLTTTTIIENFPGFPNGIDGNELMMNMRTQSEKYGTTIITETIDHVDFSTQPFKLFTEEGKEVLTKSVIIATGATAKRMHVPGEDKYWQNGVSACAICDGAVPIFRNKVLMVVGGGDAAMEEALHLTKYGSKVIILHRRDAFRASKTMQERVLNHPKIEVIWNSELVELEGDGDLLNGAKIHNLVSGEYKVVPVAGLFYAIGHSPNSKFLGGQVKTADDGYILTEGPKTSVDGVFACGDVCDRVYRQAIVAAGSGCMAALSCEKWLQTH 314
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhh....eee...hhhhh...hhhhhh.ee.........eehhhhhhhhhhhhhhh..eee...eeeee.....eeeee....eeeeeeeee...eee......hhhhhh...ee.hhhhhh.hhhhh..eeeee..hhhhhhhhhhhhh...eeeee........hhhhhhhhhh...eeee..eeeeeeee....eeeeeeee.....eeeee..eeee...eee.hhhhh......................eee.hhhh.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a65 B   2 SNIHDVVIIGSGPAAHTAAIYLGRSSLKPVMYEGFMAGGVAAGGQLTTTTIIENFPGFPNGIDGNELMMNMRTQSEKYGTTIITETIDHVDFSTQPFKLFTEEGKEVLTKSVIIATGATAKRMHVPGEDKYWQNGVSACAICDGAVPIFRNKVLMVVGGGDAAMEEALHLTKYGSKVIILHRRDAFRASKTMQERVLNHPKIEVIWNSELVELEGDGDLLNGAKIHNLVSGEYKVVPVAGLFYAIGHSPNSKFLGGQVKTADDGYILTEGPKTSVDGVFACGDVCDRVYRQAIVAAGSGCMAALSCEKWLQTH 314
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4A65)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A65)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A65)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (C4LW95_ENTHI | C4LW95)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004791    thioredoxin-disulfide reductase activity    Catalysis of the reaction: NADP(+) + thioredoxin = H(+) + NADPH + thioredoxin disulfide.
biological process
    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:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/TrEMBL
        C4LW95_ENTHI | C4LW95: 4a5l 4cbq 4ccq 4ccr 4up3

(-) Related Entries Specified in the PDB File

4a5l CRYSTAL STRUCTURE OF THE THIOREDOXIN REDUCTASE FROM ENTAMOEBA HISTOLYTICA