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(-) Description

Title :  THE STRUCTURE OF UNCHARACTERIZED PROTEIN YKR043C FROM SACCHAROMYCES CEREVISIAE.
 
Authors :  M. Cuff, X. Xu, H. Cui, A. Edwards, A. Savchenko, A. Joachimiak, Midwest For Structural Genomics (Mcsg)
Date :  30 Oct 08  (Deposition) - 09 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Saccharomyces Cerevisiae, Structural Genomics, , Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Structural Genomics, Unknown Function (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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED P11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YKR043C
    Organism Common: BREWER'S YEAST,LAGER BEER YEAST,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  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:18 , GLN A:23 , TYR A:61 , ARG A:90 , LYS A:161 , HIS A:162 , ARG A:167 , THR A:212 , HOH A:394 , HOH A:401 , HOH A:447 , HOH A:804 , HOH B:621BINDING SITE FOR RESIDUE GOL A 266
2AC2SOFTWARETRP B:18 , LEU B:30 , LYS B:161 , GLU B:165 , HOH B:461 , HOH B:609 , HOH B:825 , HOH B:930 , HOH B:932BINDING SITE FOR RESIDUE GOL B 266
3AC3SOFTWAREASN A:204 , LYS A:206 , SER A:207 , TYR A:208 , HOH A:704 , HOH B:543 , HOH B:625BINDING SITE FOR RESIDUE GOL A 267
4AC4SOFTWAREARG A:71 , ASP A:75 , HOH A:526 , HOH A:700 , HOH A:799BINDING SITE FOR RESIDUE GOL A 268
5AC5SOFTWAREGLN B:156 , ILE B:186 , TRP B:187 , ARG B:222 , PRO B:250 , HOH B:453 , HOH B:496 , HOH B:553BINDING SITE FOR RESIDUE GOL B 267
6AC6SOFTWAREASN B:204 , LYS B:206 , TYR B:208 , HOH B:416 , HOH B:419 , HOH B:492BINDING SITE FOR RESIDUE GOL B 268

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F3K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F3K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F3K)

(-) Exons   (0, 0)

(no "Exon" information available for 3F3K)

(-) 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:260
 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 3f3kA00 A:3-263 Phosphoglycerate mutase-like                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhhhh..........hhhhhhhhhhhhhhhhh.-...hhh.eeeeee..hhhhhhhhhhhh...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
                 3f3k A   3 SLTPRCIIVRHGQTEWSKSGQYTGLTDLPLTPYGEGQmLRTGESVFRN-QFLNPDNITYIFTSPRLRARQTVDLVLKPLSDEQRAKIRVVVDDDLREWEYGDYEGmLTREIIELRKSRGLDKERPWNIWRDGCENGETTQQIGLRLSRAIARIQNLHRKHQSEGRASDImVFAHGHALRYFAAIWFGLGVQKKCETIEEIQNVKSYDDDTVPYVKLESYRHLVDNPCFLLDAGGIGVLSYAHHNIDEPALELAGPFVSPPE 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 
                                                                40-MSE    50 |                                                     108-MSE                                                         172-MSE                                                                                       
                                                                            52                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with SHB17_YEAST | P36136 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:262
                                    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  
          SHB17_YEAST     2 PSLTPRCIIVRHGQTEWSKSGQYTGLTDLPLTPYGEGQMLRTGESVFRNNQFLNPDNITYIFTSPRLRARQTVDLVLKPLSDEQRAKIRVVVDDDLREWEYGDYEGMLTREIIELRKSRGLDKERPWNIWRDGCENGETTQQIGLRLSRAIARIQNLHRKHQSEGRASDIMVFAHGHALRYFAAIWFGLGVQKKCETIEEIQNVKSYDDDTVPYVKLESYRHLVDNPCFLLDAGGIGVLSYAHHNIDEPALELAGPFVSPPE 263
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f3kB00 B:2-263 Phosphoglycerate mutase-like                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...hhhhhhh..........hhhhhhhhhhhhhhhhh.....hhh.eeeeee..hhhhhhhhhhhh...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
                 3f3k B   2 PSLTPRCIIVRHGQTEWSKSGQYTGLTDLPLTPYGEGQmLRTGESVFRNNQFLNPDNITYIFTSPRLRARQTVDLVLKPLSDEQRAKIRVVVDDDLREWEYGDYEGmLTREIIELRKSRGLDKERPWNIWRDGCENGETTQQIGLRLSRAIARIQNLHRKHQSEGRASDImVFAHGHALRYFAAIWFGLGVQKKCETIEEIQNVKSYDDDTVPYVKLESYRHLVDNPCFLLDAGGIGVLSYAHHNIDEPALELAGPFVSPPE 263
                                    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  
                                                                 40-MSE                                                             108-MSE                                                         172-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 3F3K)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F3K)

(-) 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

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UniProtKB/Swiss-Prot
        SHB17_YEAST | P36136: 3lg2 3ll4 3oi7

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