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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THIOREDOXIN REDUCTASE FROM ENTAMOEBA HISTOLYTICA WITH NADP
 
Authors :  D. Parsonage, P. M. Kells, K. Hirata, A. Debnath, L. B. Poole, J. H. Mcker S. L. Reed, L. M. Podust
Date :  24 Oct 13  (Deposition) - 05 Nov 14  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Amoebiasis, Redox Metabolism, Oxidative Stress, Auranofin (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 B
    Expression System Plasmid: PTRCHISA
    Expression System Strain: B834
    Expression System Taxid: 37762
    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
1ACT1Ligand/IonACETATE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:43 , GLY A:44 , THR A:48 , MET A:69 , MET A:70 , ARG A:73 , HOH A:2020 , HOH A:2108 , HOH A:2448BINDING SITE FOR RESIDUE EDO A1315
2AC2SOFTWARELYS B:122 , GLY B:160 , GLY B:161 , ASP B:162 , ALA B:163 , HIS B:182 , ARG B:183 , ARG B:184 , ARG B:188 , ALA B:245 , ILE B:246 , TYR B:290 , ARG B:291 , GLN B:292 , HOH B:2178 , HOH B:2227 , HOH B:2228 , HOH B:2229 , HOH B:2231 , HOH B:2232 , HOH B:2243 , HOH B:2246 , HOH B:2324 , HOH B:2383 , HOH B:2404 , HOH B:2405 , HOH B:2407 , HOH B:2409 , HOH B:2410BINDING SITE FOR RESIDUE NAP B1315
3AC3SOFTWAREGLY A:160 , GLY A:161 , ASP A:162 , ALA A:163 , GLU A:166 , HIS A:182 , ARG A:183 , ARG A:184 , ARG A:188 , ALA A:245 , ILE A:246 , HOH A:2230 , HOH A:2268 , HOH A:2269 , HOH A:2283 , HOH A:2295 , HOH A:2297 , HOH A:2360 , HOH A:2361 , HOH A:2364 , HOH A:2450 , HOH A:2451 , HOH A:2452 , HOH A:2453BINDING SITE FOR RESIDUE NAP A1316
4AC4SOFTWAREGLU A:270 , THR A:274 , HOH A:2378 , HOH A:2407BINDING SITE FOR RESIDUE ACT A1317
5AC5SOFTWAREALA B:43 , GLY B:44 , THR B:48 , MET B:69 , MET B:70 , ARG B:73 , HOH B:2019 , HOH B:2103BINDING SITE FOR RESIDUE EDO B1316
6AC6SOFTWAREHOH A:2242 , LEU B:268 , LYS B:273 , THR B:274 , SER B:275 , HOH B:2343BINDING SITE FOR RESIDUE EDO B1317
7AC7SOFTWAREILE 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 , ALA A:43 , GLY A:45 , GLN A:46 , LEU A:47 , THR A:49 , THR A:50 , ASN A:55 , THR A:87 , ILE A:88 , ALA A:116 , 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:2016 , HOH A:2047 , HOH A:2073 , HOH A:2080 , HOH A:2083 , HOH A:2088 , HOH A:2224 , HOH A:2225 , HOH A:2454 , TYR B:22BINDING SITE FOR RESIDUE FAD A1318
8AC8SOFTWARETYR A:22 , HOH A:2027 , 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 , ALA B:116 , 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:2016 , HOH B:2039 , HOH B:2056 , HOH B:2064 , HOH B:2070 , HOH B:2071 , HOH B:2169 , HOH B:2171 , HOH B:2331BINDING SITE FOR RESIDUE FAD B1318

(-) 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 4CCQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CCQ)

(-) 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: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..hhhhhhhhhhhh....eeeee........hhhhhhhhhh...eeee..eeeeeeee....eeeeeeee.....eeeee..eeee...eee.hhhhh......................eee.hhhh.....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ccq A   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   


Chain B from PDB  Type:PROTEIN  Length:312
 aligned with C4LW95_ENTHI | C4LW95 from UniProtKB/TrEMBL  Length:314

    Alignment length:312
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312  
         C4LW95_ENTHI     3 NIHDVVIIGSGPAAHTAAIYLGRSSLKPVMYEGFMAGGVAAGGQLTTTTIIENFPGFPNGIDGNELMMNMRTQSEKYGTTIITETIDHVDFSTQPFKLFTEEGKEVLTKSVIIATGATAKRMHVPGEDKYWQNGVSACAICDGAVPIFRNKVLMVVGGGDAAMEEALHLTKYGSKVIILHRRDAFRASKTMQERVLNHPKIEVIWNSELVELEGDGDLLNGAKIHNLVSGEYKVVPVAGLFYAIGHSPNSKFLGGQVKTADDGYILTEGPKTSVDGVFACGDVCDRVYRQAIVAAGSGCMAALSCEKWLQTH 314
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh....eee...hhhhh...hhhhhh.ee.........eehhhhhhhhhhhhhhh..eee...eeeee.....eeeee....eeeeeeeee...eee......hhhhhh...ee.hhhhhh.hhhhh..eeeee..hhhhhhhhhhhh....eeeee........hhhhhhhhhhh..eeee..eeeeeeee....eeeeeeee.....eeeee..eeee...eee.hhhhh......................eee.hhhh.....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ccq B   3 NIHDVVIIGSGPAAHTAAIYLGRSSLKPVMYEGFMAGGVAAGGQLTTTTIIENFPGFPNGIDGNELMMNMRTQSEKYGTTIITETIDHVDFSTQPFKLFTEEGKEVLTKSVIIATGATAKRMHVPGEDKYWQNGVSACAICDGAVPIFRNKVLMVVGGGDAAMEEALHLTKYGSKVIILHRRDAFRASKTMQERVLNHPKIEVIWNSELVELEGDGDLLNGAKIHNLVSGEYKVVPVAGLFYAIGHSPNSKFLGGQVKTADDGYILTEGPKTSVDGVFACGDVCDRVYRQAIVAAGSGCMAALSCEKWLQTH 314
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
   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 4CCQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4a65 4cbq 4ccr 4up3

(-) Related Entries Specified in the PDB File

4ccr CRYSTAL STRUCTURE OF THE THIOREDOXIN REDUCTASE APOENZYME FROM ENTAMOEBA HISTOLYTICA IN THE ABSENCE OF THE NADP COFACTOR