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(-) Description

Title :  CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN PH0414 FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  H. Yamamoto, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Jul 06  (Deposition) - 26 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yamamoto, N. Kunishima
Crystal Structure Of Hypothetical Protein Ph0414 From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 336AA LONG HYPOTHETICAL DTDP-GLUCOSE 4,6-DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , MET A:12 , GLY A:13 , PHE A:14 , ILE A:15 , ASP A:36 , LYS A:37 , LEU A:38 , GLY A:39 , SER A:42 , GLY A:61 , ASP A:62 , VAL A:63 , LEU A:82 , ALA A:83 , ALA A:84 , SER A:101 , VAL A:125 , SER A:126 , THR A:127 , TYR A:151 , LYS A:155 , CYS A:178 , THR A:179 , ASN A:180 , ASN A:181 , HOH A:822 , HOH A:825 , HOH A:826 , HOH A:831 , HOH A:857 , HOH A:916 , HOH A:918 , HOH A:919 , HOH A:959 , HOH A:1041BINDING SITE FOR RESIDUE NAD A 801
2AC2SOFTWAREGLY B:10 , MET B:12 , GLY B:13 , PHE B:14 , ILE B:15 , ASP B:36 , LYS B:37 , LEU B:38 , GLY B:39 , SER B:42 , GLY B:61 , ASP B:62 , VAL B:63 , LEU B:82 , ALA B:83 , ALA B:84 , SER B:86 , SER B:101 , VAL B:125 , SER B:126 , THR B:127 , TYR B:151 , LYS B:155 , CYS B:178 , THR B:179 , ASN B:180 , ASN B:181 , HOH B:811 , HOH B:824 , HOH B:828 , HOH B:829 , HOH B:842 , HOH B:896 , HOH B:1012BINDING SITE FOR RESIDUE NAD B 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HUN)

(-) 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:329
 aligned with O58151_PYRHO | O58151 from UniProtKB/TrEMBL  Length:336

    Alignment length:332
                                    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  
         O58151_PYRHO     3 SMKLLVTGGMGFIGSNFIRYILEKHPDWEVINIDKLGYGSNPANLKDLEDDPRYTFVKGDVADYELVKELVRKVDGVVHLAAESHVDRSISSPEIFLHSNVIGTYTLLESIRRENPEVRFVHVSTDEVYGDILKGSFTENDRLMPSSPYSATKAASDMLVLGWTRTYNLNASITRCTNNYGPYQFPEKLIPKTIIRASLGLKIPIYGTGKNVRDWLYVEDHVRAIELVLLKGESREIYNISAGEEKTNLEVVKIILRLMGKGEELIELVEDRPGHDLRYSLDSWKITRDLKWRPKYTFDEGIKKTIDWYLKNEWWWKPLVDERILHPTPWKL 334
               SCOP domains d2huna_ A: automated matches                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2hunA01 A:3-179,A:220-242,A:279-297 NAD(P)-binding Rossmann-like Domain                                                                                                          2hunA02 A:180-219,A:243-278,A:2   98-3342hunA01                2hunA02                             2hunA01            2hunA02 A:180-219,A:243-278,A:298-334 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhh...eeeeee......hhhhhh.......eeeee....hhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhh..eeeeeee.eee.......hhhhhhhhhhhh...eeee..---.eeeeehhhhhhhhhhhhhhh....eeee....eehhhhhhhhhhhhh......eeee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hun A   3 SMKLLVTGGMGFIGSNFIRYILEKHPDWEVINIDKLGYGSNPANLKDLEDDPRYTFVKGDVADYELVKELVRKVDGVVHLAAESHVDRSISSPEIFLHSNVIGTYTLLESIRRENPEVRFVHVSTDEVYGDILKGSFTENDRLMPSSPYSATKAASDMLVLGWTRTYNLNASITRCTNNYGPYQFPEKLIPKTIIRASLGLKIPIYGT---VRDWLYVEDHVRAIELVLLKGESREIYNISAGEEKTNLEVVKIILRLMGKGEELIELVEDRPGHDLRYSLDSWKITRDLKWRPKYTFDEGIKKTIDWYLKNEWWWKPLVDERILHPTPWKL 334
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       | - |     222       232       242       252       262       272       282       292       302       312       322       332  
                                                                                                                                                                                                                                         210 214                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:325
 aligned with O58151_PYRHO | O58151 from UniProtKB/TrEMBL  Length:336

    Alignment length:325
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320     
         O58151_PYRHO     1 MHSMKLLVTGGMGFIGSNFIRYILEKHPDWEVINIDKLGYGSNPANLKDLEDDPRYTFVKGDVADYELVKELVRKVDGVVHLAAESHVDRSISSPEIFLHSNVIGTYTLLESIRRENPEVRFVHVSTDEVYGDILKGSFTENDRLMPSSPYSATKAASDMLVLGWTRTYNLNASITRCTNNYGPYQFPEKLIPKTIIRASLGLKIPIYGTGKNVRDWLYVEDHVRAIELVLLKGESREIYNISAGEEKTNLEVVKIILRLMGKGEELIELVEDRPGHDLRYSLDSWKITRDLKWRPKYTFDEGIKKTIDWYLKNEWWWKPLVDER 325
               SCOP domains d2hunb_ B: automated matches                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2hunB01 B:1-179,B:220-242,B:279-297 NAD(P)-binding Rossmann-like Domain                                                                                                            2hunB02 B:180-219,B:243-278,B:298-325   2hunB01                2hunB02                             2hunB01            2hunB02                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhh...eeeeee......hhhhhh.......eeeee....hhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhh..eeeeeee.eee.......hhhhhhhhhhh....eeee.....eeeeeehhhhhhhhhhhhhhh....eeee....eeehhhhhhhhhhhhh.....eeee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hun B   1 MHSMKLLVTGGMGFIGSNFIRYILEKHPDWEVINIDKLGYGSNPANLKDLEDDPRYTFVKGDVADYELVKELVRKVDGVVHLAAESHVDRSISSPEIFLHSNVIGTYTLLESIRRENPEVRFVHVSTDEVYGDILKGSFTENDRLMPSSPYSATKAASDMLVLGWTRTYNLNASITRCTNNYGPYQFPEKLIPKTIIRASLGLKIPIYGTGKNVRDWLYVEDHVRAIELVLLKGESREIYNISAGEEKTNLEVVKIILRLMGKGEELIELVEDRPGHDLRYSLDSWKITRDLKWRPKYTFDEGIKKTIDWYLKNEWWWKPLVDER 325
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
   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  (1, 2)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O58151_PYRHO | O58151)
molecular function
    GO:0008460    dTDP-glucose 4,6-dehydratase activity    Catalysis of the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H(2)O.
    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.
biological process
    GO:0009225    nucleotide-sugar metabolic process    The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.

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