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(-) Description

Title :  CRYSTAL STRUCTURE OF TT0321 FROM THERMUS THERMOPHILUS HB8
 
Authors :  Y. Asada, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 Sep 05  (Deposition) - 02 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Strucrtural Genomics, Thermus Thermophilus Hb8, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Asada, N. Kunishima
Crystal Structure Of Tt0321 From Thermus Thermophilus Hb8
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TT0321
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , ARG A:16 , GLY A:17 , ILE A:18 , ASP A:37 , LEU A:38 , ARG A:39 , VAL A:56 , ASP A:57 , LEU A:58 , ASN A:84 , ALA A:85 , ALA A:86 , ILE A:87 , VAL A:134 , ALA A:135 , SER A:136 , TYR A:149 , LYS A:153 , PRO A:179 , GLY A:180 , ILE A:182 , THR A:184 , ALA A:186 , VAL A:187 , HOH A:1028 , HOH A:1044 , HOH A:1096 , HOH A:1104BINDING SITE FOR RESIDUE NAD A 1001
2AC2SOFTWAREGLY B:13 , ARG B:16 , GLY B:17 , ILE B:18 , ASP B:37 , LEU B:38 , ARG B:39 , VAL B:56 , ASP B:57 , LEU B:58 , ASN B:84 , ALA B:85 , ALA B:86 , ILE B:87 , VAL B:134 , ALA B:135 , SER B:136 , TYR B:149 , LYS B:153 , PRO B:179 , GLY B:180 , ILE B:182 , THR B:184 , VAL B:187 , HOH B:1043 , HOH B:1079 , HOH B:1090 , HOH B:1127BINDING SITE FOR RESIDUE NAD B 1002
3AC3SOFTWAREGLY C:13 , ARG C:16 , GLY C:17 , ILE C:18 , ASP C:37 , LEU C:38 , ARG C:39 , VAL C:56 , ASP C:57 , LEU C:58 , ASN C:84 , ALA C:85 , ALA C:86 , ILE C:87 , VAL C:134 , ALA C:135 , SER C:136 , TYR C:149 , LYS C:153 , PRO C:179 , GLY C:180 , ALA C:181 , ILE C:182 , THR C:184 , ALA C:186 , VAL C:187 , HOH C:1006 , HOH C:1007 , HOH C:1049 , HOH C:1077 , HOH C:1150BINDING SITE FOR RESIDUE NAD C 1003
4AC4SOFTWAREGLY D:13 , ARG D:16 , GLY D:17 , ILE D:18 , ASP D:37 , LEU D:38 , ARG D:39 , VAL D:56 , ASP D:57 , LEU D:58 , ASN D:84 , ALA D:85 , ALA D:86 , ILE D:87 , VAL D:134 , ALA D:135 , SER D:136 , TYR D:149 , LYS D:153 , PRO D:179 , GLY D:180 , ALA D:181 , ILE D:182 , THR D:184 , ALA D:186 , VAL D:187 , HOH D:1020 , HOH D:1039 , HOH D:1052 , HOH D:1109 , HOH D:1157BINDING SITE FOR RESIDUE NAD D 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D1Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D1Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2D1Y)

(-) 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:240
 aligned with Q5SLC4_THET8 | Q5SLC4 from UniProtKB/TrEMBL  Length:256

    Alignment length:248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
         Q5SLC4_THET8     2 GLFAGKGVLVTGGARGIGRAIAQAFAREGALVALCDLRPEGKEVAEAIGGAFFQVDLEDERERVRFVEEAAYALGRVDVLVNNAAIAAPGSALTVRLPEWRRVLEVNLTAPMHLSALAAREMRKVGGGAIVNVASVQGLFAEQENAAYNASKGGLVNLTRSLALDLAPLRIRVNAVAPGAIATEAVLEAIALSPDPERTRRDWEDLHALRRLGKPEEVAEAVLFLASEKASFITGAILPVDGGMTASF 249
               SCOP domains d2d1ya1 A:2-249 Hypothetical protein TTHA0369                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhh--------hhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1y A   2 GLFAGKGVLVTGGARGIGRAIAQAFAREGALVALCDLRPEGKEVAEAIGGAFFQVDLEDERERVRFVEEAAYALGRVDVLVNNAAIAAPGSALTVRLPEWRRVLEVNLTAPMHLSALAAREMRKVGGGAIVNVASVQGLFAEQENAAYNASKGGLVNLTRSLALDLAPLRIRVNAVAPGAIATEAVLEAIA--------RRDWEDLHALRRLGKPEEVAEAVLFLASEKASFITGAILPVDGGMTASF 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191|      201       211       221       231       241        
                                                                                                                                                                                                                        192      201                                                


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with Q5SLC4_THET8 | Q5SLC4 from UniProtKB/TrEMBL  Length:256

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
         Q5SLC4_THET8     2 GLFAGKGVLVTGGARGIGRAIAQAFAREGALVALCDLRPEGKEVAEAIGGAFFQVDLEDERERVRFVEEAAYALGRVDVLVNNAAIAAPGSALTVRLPEWRRVLEVNLTAPMHLSALAAREMRKVGGGAIVNVASVQGLFAEQENAAYNASKGGLVNLTRSLALDLAPLRIRVNAVAPGAIATEAVLEAIALSPDPERTRRDWEDLHALRRLGKPEEVAEAVLFLASEKASFITGAILPVDGGMTASFM 250
               SCOP domains d2d1yb_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhh-------hhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1y B   2 GLFAGKGVLVTGGARGIGRAIAQAFAREGALVALCDLRPEGKEVAEAIGGAFFQVDLEDERERVRFVEEAAYALGRVDVLVNNAAIAAPGSALTVRLPEWRRVLEVNLTAPMHLSALAAREMRKVGGGAIVNVASVQGLFAEQENAAYNASKGGLVNLTRSLALDLAPLRIRVNAVAPGAIATEAVLEAI-------RTRRDWEDLHALRRLGKPEEVAEAVLFLASEKASFITGAILPVDGGMTASFM 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
                                                                                                                                                                                                                       191     199                                                   


Chain C from PDB  Type:PROTEIN  Length:248
 aligned with Q5SLC4_THET8 | Q5SLC4 from UniProtKB/TrEMBL  Length:256

    Alignment length:248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
         Q5SLC4_THET8     2 GLFAGKGVLVTGGARGIGRAIAQAFAREGALVALCDLRPEGKEVAEAIGGAFFQVDLEDERERVRFVEEAAYALGRVDVLVNNAAIAAPGSALTVRLPEWRRVLEVNLTAPMHLSALAAREMRKVGGGAIVNVASVQGLFAEQENAAYNASKGGLVNLTRSLALDLAPLRIRVNAVAPGAIATEAVLEAIALSPDPERTRRDWEDLHALRRLGKPEEVAEAVLFLASEKASFITGAILPVDGGMTASF 249
               SCOP domains d2d1yc_ C: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1y C   2 GLFAGKGVLVTGGARGIGRAIAQAFAREGALVALCDLRPEGKEVAEAIGGAFFQVDLEDERERVRFVEEAAYALGRVDVLVNNAAIAAPGSALTVRLPEWRRVLEVNLTAPMHLSALAAREMRKVGGGAIVNVASVQGLFAEQENAAYNASKGGLVNLTRSLALDLAPLRIRVNAVAPGAIATEAVLEAIALSPDPERTRRDWEDLHALRRLGKPEEVAEAVLFLASEKASFITGAILPVDGGMTASF 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        


Chain D from PDB  Type:PROTEIN  Length:240
 aligned with Q5SLC4_THET8 | Q5SLC4 from UniProtKB/TrEMBL  Length:256

    Alignment length:247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       
         Q5SLC4_THET8     3 LFAGKGVLVTGGARGIGRAIAQAFAREGALVALCDLRPEGKEVAEAIGGAFFQVDLEDERERVRFVEEAAYALGRVDVLVNNAAIAAPGSALTVRLPEWRRVLEVNLTAPMHLSALAAREMRKVGGGAIVNVASVQGLFAEQENAAYNASKGGLVNLTRSLALDLAPLRIRVNAVAPGAIATEAVLEAIALSPDPERTRRDWEDLHALRRLGKPEEVAEAVLFLASEKASFITGAILPVDGGMTASF 249
               SCOP domains d2d1yd_ D: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhh.-------hhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1y D   3 LFAGKGVLVTGGARGIGRAIAQAFAREGALVALCDLRPEGKEVAEAIGGAFFQVDLEDERERVRFVEEAAYALGRVDVLVNNAAIAAPGSALTVRLPEWRRVLEVNLTAPMHLSALAAREMRKVGGGAIVNVASVQGLFAEQENAAYNASKGGLVNLTRSLALDLAPLRIRVNAVAPGAIATEAVLEAIA-------TRRDWEDLHALRRLGKPEEVAEAVLFLASEKASFITGAILPVDGGMTASF 249
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       
                                                                                                                                                                                                                       192     200
   Legend:   → Mismatch (orange background)
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  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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D1Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D1Y)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SLC4_THET8 | Q5SLC4)
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.
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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