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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PH0510 PROTEIN FROM PYROCOCCUS HORIKOSHII OT3 IN COMPLEX WITH BETA-D-FRUCTOPYRANOSE-1-PHOSPHATE
 
Authors :  H. Mizutani, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  27 Feb 06  (Deposition) - 27 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Sugar Binding Protein, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, N. Kunishima
Crystal Structure Of The Ph0510 Protein From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 325AA LONG HYPOTHETICAL PROTEIN
    Chains: A, B
    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
    Synonym: PH0510 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2F1P2Ligand/Ion1-O-PHOSPHONO-BETA-D-FRUCTOPYRANOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:39 , SER A:41 , SER A:42 , SER A:87 , ARG A:88 , SER A:89 , THR A:92 , VAL A:133 , GLU A:211 , ASP A:320 , LYS A:321 , HOH A:906 , HOH A:907 , HOH A:910 , HOH A:913 , HOH A:916 , HOH A:1167 , HIS B:227BINDING SITE FOR RESIDUE F1P A 801
2AC2SOFTWAREHIS A:227 , CYS B:39 , SER B:41 , SER B:42 , SER B:87 , ARG B:88 , SER B:89 , THR B:92 , VAL B:133 , GLU B:211 , ASP B:320 , LYS B:321 , VAL B:323 , HOH B:910 , HOH B:916 , HOH B:924 , HOH B:927 , HOH B:939 , HOH B:1061BINDING SITE FOR RESIDUE F1P B 802
3AC3SOFTWARELEU A:159 , ASN A:160 , GLU A:163 , ILE A:164 , LEU A:285 , SER A:286 , HOH A:1159BINDING SITE FOR RESIDUE EDO A 901
4AC4SOFTWARELYS A:105 , VAL B:182 , GLU B:183 , ASP B:186 , HOH B:1019BINDING SITE FOR RESIDUE EDO B 902
5AC5SOFTWARELYS A:47 , HOH A:945BINDING SITE FOR RESIDUE EDO A 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DF8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DF8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DF8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DF8)

(-) Exons   (0, 0)

(no "Exon" information available for 2DF8)

(-) 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:325
 aligned with O58246_PYRHO | O58246 from UniProtKB/TrEMBL  Length:325

    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     
         O58246_PYRHO     1 MKTLIEIKQTPDGIIKADKVFNKVKDKISLPNRILYLGCGSSHFLSKLLAMVTNMHGGLGIALPCSEFLYSKETYPIGEVELAVGISRSGETTEILLALEKINVKKLGITTRESSLTRMCDYSLVVPAIEESVVMTHSFTSFYFAYLQLLRYSYGLPPLNAGEISKATEKSLEYERYIREIVESFDFQNIIFLGSGLLYPVALEASLKMKEMSIFWSEAYPTFEVRHGFKAIADEKTLVVLMVEEPFEWHEKLVKEFKNQGAKVLVISNSPQDLGQDYSIELPRLSKDANPIPYLPIVQLLSYYKAVSRGLNPDNPRFLDKVVRW 325
               SCOP domains d2df8a_ A: automated matches                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh......eeeee.....hhhhhhhhh.....eeeee...hhhhhh..eeee..........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhh..eeeeee.........eeee...........hhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2df8 A   1 MKTLIEIKQTPDGIIKADKVFNKVKDKISLPNRILYLGCGSSHFLSKLLAMVTNMHGGLGIALPCSEFLYSKETYPIGEVELAVGISRSGETTEILLALEKINVKKLGITTRESSLTRMCDYSLVVPAIEESVVMTHSFTSFYFAYLQLLRYSYGLPPLNAGEISKATEKSLEYERYIREIVESFDFQNIIFLGSGLLYPVALEASLKMKEMSIFWSEAYPTFEVRHGFKAIADEKTLVVLMVEEPFEWHEKLVKEFKNQGAKVLVISNSPQDLGQDYSIELPRLSKDANPIPYLPIVQLLSYYKAVSRGLNPDNPRFLDKVVRW 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     


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with O58246_PYRHO | O58246 from UniProtKB/TrEMBL  Length:325

    Alignment length:324
                                    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    
         O58246_PYRHO     2 KTLIEIKQTPDGIIKADKVFNKVKDKISLPNRILYLGCGSSHFLSKLLAMVTNMHGGLGIALPCSEFLYSKETYPIGEVELAVGISRSGETTEILLALEKINVKKLGITTRESSLTRMCDYSLVVPAIEESVVMTHSFTSFYFAYLQLLRYSYGLPPLNAGEISKATEKSLEYERYIREIVESFDFQNIIFLGSGLLYPVALEASLKMKEMSIFWSEAYPTFEVRHGFKAIADEKTLVVLMVEEPFEWHEKLVKEFKNQGAKVLVISNSPQDLGQDYSIELPRLSKDANPIPYLPIVQLLSYYKAVSRGLNPDNPRFLDKVVRW 325
               SCOP domains d2df8b_ B: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh......eeeee.....hhhhhhhhhh....eeeee...hhhhhh..eeee..........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhh..eeeeee.........eeee...........hhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2df8 B   2 KTLIEIKQTPDGIIKADKVFNKVKDKISLPNRILYLGCGSSHFLSKLLAMVTNMHGGLGIALPCSEFLYSKETYPIGEVELAVGISRSGETTEILLALEKINVKKLGITTRESSLTRMCDYSLVVPAIEESVVMTHSFTSFYFAYLQLLRYSYGLPPLNAGEISKATEKSLEYERYIREIVESFDFQNIIFLGSGLLYPVALEASLKMKEMSIFWSEAYPTFEVRHGFKAIADEKTLVVLMVEEPFEWHEKLVKEFKNQGAKVLVISNSPQDLGQDYSIELPRLSKDANPIPYLPIVQLLSYYKAVSRGLNPDNPRFLDKVVRW 325
                                    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
   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  (0, 0)

(no "CATH Domain" information available for 2DF8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DF8)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O58246_PYRHO | O58246)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.

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 Related Entries

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

UniProtKB/TrEMBL
        O58246_PYRHO | O58246: 2dec 2e5f

(-) Related Entries Specified in the PDB File

2dec THE SAME PROTEIN IN APO FORM RELATED ID: PHO001000510.3 RELATED DB: TARGETDB