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(-) Description

Title :  CRYSTAL STRUCTURE OF THIOREDOXIN REDUCTASE-LIKE PROTEIN FROM THERMUS THERMOPHILUS HB8
 
Authors :  A. Ebihara, M. Manzoku, Y. Fujimoto, Y. Kitamura, S. Yokoyama, S. Kuram Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Oct 07  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Redox Protein, Oxidoreductase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ebihara, M. Manzoku, Y. Fujimoto, Y. Kitamura, S. Yokoyama, S. Kuramitsu
Crystal Structure Of Thioredoxin Reductase-Like Protein Fro Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THIOREDOXIN REDUCTASE
    Chains: A, B
    EC Number: 1.8.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:326 , SER A:327 , SER A:328 , GLU A:329 , HOH A:1024 , VAL B:11 , GLY B:12 , GLY B:14 , PRO B:15 , THR B:16 , VAL B:34 , ASP B:35 , PRO B:36 , GLY B:42 , GLN B:43 , LEU B:44 , TYR B:48 , ILE B:53 , ASP B:55 , ARG B:87 , ALA B:88 , ALA B:116 , ALA B:117 , GLY B:118 , GLY B:120 , ALA B:121 , PHE B:122 , GLY B:286 , ASP B:287 , PRO B:296 , LEU B:297 , ILE B:298 , HOH B:1002 , HOH B:1003 , HOH B:1007 , HOH B:1008 , HOH B:1018BINDING SITE FOR RESIDUE FAD B 1001
2AC2SOFTWAREVAL A:11 , GLY A:12 , GLY A:14 , PRO A:15 , THR A:16 , VAL A:34 , ASP A:35 , PRO A:36 , LEU A:37 , GLY A:42 , GLN A:43 , LEU A:44 , TYR A:48 , ILE A:53 , ASP A:55 , ARG A:87 , ALA A:88 , ALA A:116 , ALA A:117 , GLY A:118 , GLY A:120 , ALA A:121 , PHE A:122 , GLY A:286 , ASP A:287 , PRO A:296 , ILE A:298 , HOH A:1005 , HOH A:1010 , HOH A:1014 , HOH A:1015 , HOH A:1030 , HIS B:326 , SER B:327 , SER B:328 , GLU B:329BINDING SITE FOR RESIDUE FAD A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZBW)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:210 -Pro A:211
2Thr B:210 -Pro B:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZBW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZBW)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZBW)

(-) 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:333
 aligned with FENR_THET8 | Q5SL28 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:333
                                    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       322       332   
           FENR_THET8     3 ADHTDVLIVGAGPTGLFAGFYVGMRGLSFRFVDPLPEPGGQLTALYPEKYIYDVAGFPKVYAKDLVKGLVEQVAPFNPVYSLGERAETLEREGDLFKVTTSQGNAYTAKAVIIAAGVGAFEPRRIGAPGEREFEGRGVYYAVKSKAEFQGKRVLIVGGGDSAVDWALNLLDTARRITLIHRRPQFRAHEASVKELMKAHEEGRLEVLTPYELRRVEGDERVRWAVVFHNQTQEELALEVDAVLILAGYITKLGPLANWGLALEKNKIKVDTTMATSIPGVYACGDIVTYPGKLPLIVLGFGEAAIAANHAAAYANPALKVNPGHSSEKAAPGT 335
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zbwA01 A:3-125,A:249-335  [code=3.50.50.60, no name defined]                                                              2zbwA02 A:126-248  [code=3.50.50.60, no name defined]                                                                      2zbwA01 A:3-125,A:249-335  [code=3.50.50.60, no name defined]                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhh...eeeee.....hhhhhhh....ee........eehhhhhhhhhhhhhhhh.eeee...eeeeeee..eeeeee....eeeeeeeee.....eeee...............ee....hhhhhh..eeeee..hhhhhhhhhhh.....eeeee........hhhhhhhhhhhhhh...eee..eeeeeeee...eeeeeeee.....eeeee..eeee...eeeehhhhhhh...ee..eee...........eee....ee......hhhhhhhhhhhhhhhhhhhhh........hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zbw A   3 ADHTDVLIVGAGPTGLFAGFYVGmRGLSFRFVDPLPEPGGQLTALYPEKYIYDVAGFPKVYAKDLVKGLVEQVAPFNPVYSLGERAETLEREGDLFKVTTSQGNAYTAKAVIIAAGVGAFEPRRIGAPGEREFEGRGVYYAVKSKAEFQGKRVLIVGGGDSAVDWALNLLDTARRITLIHRRPQFRAHEASVKELmKAHEEGRLEVLTPYELRRVEGDERVRWAVVFHNQTQEELALEVDAVLILAGYITKLGPLANWGLALEKNKIKVDTTmATSIPGVYACGDIVTYPGKLPLIVLGFGEAAIAANHAAAYANPALKVNPGHSSEKAAPGT 335
                                    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       322       332   
                                                  26-MSE                                                                                                                                                                     198-MSE                                                                      275-MSE                                                        


Chain B from PDB  Type:PROTEIN  Length:334
 aligned with FENR_THET8 | Q5SL28 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:334
                                    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       321       331    
           FENR_THET8     2 AADHTDVLIVGAGPTGLFAGFYVGMRGLSFRFVDPLPEPGGQLTALYPEKYIYDVAGFPKVYAKDLVKGLVEQVAPFNPVYSLGERAETLEREGDLFKVTTSQGNAYTAKAVIIAAGVGAFEPRRIGAPGEREFEGRGVYYAVKSKAEFQGKRVLIVGGGDSAVDWALNLLDTARRITLIHRRPQFRAHEASVKELMKAHEEGRLEVLTPYELRRVEGDERVRWAVVFHNQTQEELALEVDAVLILAGYITKLGPLANWGLALEKNKIKVDTTMATSIPGVYACGDIVTYPGKLPLIVLGFGEAAIAANHAAAYANPALKVNPGHSSEKAAPGT 335
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zbwB01 B:2-125,B:249-335  [code=3.50.50.60, no name defined]                                                               2zbwB02 B:126-248  [code=3.50.50.60, no name defined]                                                                      2zbwB01 B:2-125,B:249-335  [code=3.50.50.60, no name defined]                           CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-2zbwB01 B:154-234                                                      ----------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-2zbwB02 B:154-234                                                      ----------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----Pyr_redox_2-2zbwB03 B:7-293                                                                                                                                                                                                                                                                    ------------------------------------------ Pfam domains (3)
           Pfam domains (4) -----Pyr_redox_2-2zbwB04 B:7-293                                                                                                                                                                                                                                                                    ------------------------------------------ Pfam domains (4)
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhh...eeeee.....hhhhhhhh...ee........eehhhhhhhhhhhhhhhh.eeee...eeeeeee..eeeeee....eeeeeeeee.....eeee...............ee....hhhhhh..eeeee..hhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhh...eee..eeeeeeee...eeeeeeee.....eeeee..eeee...eeeehhhhhhh...ee..eee...........eee....ee......hhhhhhhhhhhhhhhhhhhhh........hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zbw B   2 AADHTDVLIVGAGPTGLFAGFYVGmRGLSFRFVDPLPEPGGQLTALYPEKYIYDVAGFPKVYAKDLVKGLVEQVAPFNPVYSLGERAETLEREGDLFKVTTSQGNAYTAKAVIIAAGVGAFEPRRIGAPGEREFEGRGVYYAVKSKAEFQGKRVLIVGGGDSAVDWALNLLDTARRITLIHRRPQFRAHEASVKELmKAHEEGRLEVLTPYELRRVEGDERVRWAVVFHNQTQEELALEVDAVLILAGYITKLGPLANWGLALEKNKIKVDTTmATSIPGVYACGDIVTYPGKLPLIVLGFGEAAIAANHAAAYANPALKVNPGHSSEKAAPGT 335
                                    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       321       331    
                                                   26-MSE                                                                                                                                                                     198-MSE                                                                      275-MSE
   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 2ZBW)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FENR_THET8 | Q5SL28)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004324    ferredoxin-NADP+ reductase activity    Catalysis of the reaction: reduced ferredoxin + NADP+ = oxidized ferredoxin + NADPH + H+.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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.
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.

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