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(-) Description

Title :  STRUCTURE OF THE H13A MUTANT OF YKR043C IN COMPLEX WITH FRUCTOSE-1,6-BISPHOSPHATE
 
Authors :  A. Singer, X. Xu, H. Cui, A. Dong, P. J. Stogios, A. M. Edwards, A. Joachim A. Savchenko, A. F. Yakunin, Midwest Center For Structural Genom (Mcsg)
Date :  28 Jan 10  (Deposition) - 09 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fructose-1, 6-Bisphosphatase, 1, 6-Fructose Diphosphate (Linear Form), Ykr043C, Saccharomyces Cerevisiae, Metal-Independent, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Kuznetsova, L. Xu, A. Singer, G. Brown, A. Dong, R. Flick, H. Cui, M. Cuff, A. Joachimiak, A. Savchenko, A. F. Yakunin
Structure And Activity Of The Metal-Independent Fructose-1, 6-Bisphosphatase Yk23 From Saccharomyces Cerevisiae.
J. Biol. Chem. V. 285 21049 2010
PubMed-ID: 20427268  |  Reference-DOI: 10.1074/JBC.M110.118315

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN YKR043C
    Chains: A, B
    EC Number: 3.1.3.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TVLIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YKR043C
    Mutation: YES
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: S288C

 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
12FP2Ligand/Ion1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , SER A:19 , TYR A:24 , THR A:25 , ARG A:69 , GLU A:99 , TYR A:102 , HIS A:176 , GLY A:177 , HIS A:178 , ARG A:181 , HOH A:279 , HOH A:281 , HIS B:244BINDING SITE FOR RESIDUE 2FP A 301
2AC2SOFTWAREHIS A:244 , ARG B:12 , SER B:19 , TYR B:24 , THR B:25 , ARG B:69 , GLU B:99 , TYR B:102 , HIS B:176 , GLY B:177 , HIS B:178 , ARG B:181BINDING SITE FOR RESIDUE 2FP B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LL4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LL4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LL4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LL4)

(-) Exons   (0, 0)

(no "Exon" information available for 3LL4)

(-) 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:261
 aligned with SHB17_YEAST | P36136 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:261
                                    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 
          SHB17_YEAST     3 SLTPRCIIVRHGQTEWSKSGQYTGLTDLPLTPYGEGQMLRTGESVFRNNQFLNPDNITYIFTSPRLRARQTVDLVLKPLSDEQRAKIRVVVDDDLREWEYGDYEGMLTREIIELRKSRGLDKERPWNIWRDGCENGETTQQIGLRLSRAIARIQNLHRKHQSEGRASDIMVFAHGHALRYFAAIWFGLGVQKKCETIEEIQNVKSYDDDTVPYVKLESYRHLVDNPCFLLDAGGIGVLSYAHHNIDEPALELAGPFVSPPE 263
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhhh...........hhhhhhhhhhhhhhhhh.....hhh.eeeeee..hhhhhhhhhhhhh..hhhhhhh.eeee.hhhh...hhhhh..hhhhhhhhhhhh........hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhh...eeee..hhhhhh................eeee......ee.....eeeeee.......eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ll4 A   3 SLTPRCIIVRAGQTEWSKSGQYTGLTDLPLTPYGEGQMLRTGESVFRNNQFLNPDNITYIFTSPRLRARQTVDLVLKPLSDEQRAKIRVVVDDDLREWEYGDYEGMLTREIIELRKSRGLDKERPWNIWRDGCENGETTQQIGLRLSRAIARIQNLHRKHQSEGRASDIMVFAHGHALRYFAAIWFGLGVQKKCETIEEIQNVKSYDDDTVPYVKLESYRHLVDNPCFLLDAGGIGVLSYAHHNIDEPALELAGPFVSPPE 263
                                    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 


Chain B from PDB  Type:PROTEIN  Length:261
 aligned with SHB17_YEAST | P36136 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:261
                                    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 
          SHB17_YEAST     3 SLTPRCIIVRHGQTEWSKSGQYTGLTDLPLTPYGEGQMLRTGESVFRNNQFLNPDNITYIFTSPRLRARQTVDLVLKPLSDEQRAKIRVVVDDDLREWEYGDYEGMLTREIIELRKSRGLDKERPWNIWRDGCENGETTQQIGLRLSRAIARIQNLHRKHQSEGRASDIMVFAHGHALRYFAAIWFGLGVQKKCETIEEIQNVKSYDDDTVPYVKLESYRHLVDNPCFLLDAGGIGVLSYAHHNIDEPALELAGPFVSPPE 263
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhhh...........hhhhhhhhhhhhhhhhh.....hhh.eeeeee..hhhhhhhhhhhhh..hhhhhhh.eeee.hhhh...hhhhh..hhhhhhhhhhhh........hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhh...eeee..hhhhhh................eeee......ee.....eeeeee.hhh...eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ll4 B   3 SLTPRCIIVRAGQTEWSKSGQYTGLTDLPLTPYGEGQMLRTGESVFRNNQFLNPDNITYIFTSPRLRARQTVDLVLKPLSDEQRAKIRVVVDDDLREWEYGDYEGMLTREIIELRKSRGLDKERPWNIWRDGCENGETTQQIGLRLSRAIARIQNLHRKHQSEGRASDIMVFAHGHALRYFAAIWFGLGVQKKCETIEEIQNVKSYDDDTVPYVKLESYRHLVDNPCFLLDAGGIGVLSYAHHNIDEPALELAGPFVSPPE 263
                                    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
   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 3LL4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LL4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LL4)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SHB17_YEAST | P36136)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0050278    sedoheptulose-bisphosphatase activity    Catalysis of the reaction: sedoheptulose 1,7-bisphosphate + H2O = sedoheptulose 7-phosphate + phosphate.
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.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    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:0046390    ribose phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of ribose phosphate, any phosphorylated ribose sugar.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SHB17_YEAST | P36136: 3f3k 3lg2 3oi7

(-) Related Entries Specified in the PDB File

3f3k
3lg2 RELATED ID: APC7730 RELATED DB: TARGETDB