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(-) Description

Title :  STRUCTURE OF DUF89 FROM SACCHAROMYCES CEREVISIAE CO-CRYSTALLIZED WITH F6P.
 
Authors :  P. Petit, X. Xu, H. Cui, A. Savchenko, A. F. Yakunin
Date :  02 Dec 10  (Deposition) - 15 Dec 10  (Release) - 15 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Fold, Carbohydrate Phosphatase, F6P Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Brown, X. Xu, P. Petit, H. Cui, R. Flick, M. Cuff, A. Savchenko, A. F. Yakunin
Structure And Activity Of A Duf89 Protein From Saccharomyce Cerevisiae Revealed A Novel Family Of Carbohydrate Phosphatases
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UPF0364 PROTEIN YMR027W
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YM9711.17, YMR027W
    Organism Common: BREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1F6P1Ligand/IonFRUCTOSE-6-PHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:190 , ALA A:193 , THR A:194 , ASP A:195 , SER A:219 , HOH A:701 , HOH A:739BINDING SITE FOR RESIDUE GOL A 1000
2AC2SOFTWARETHR A:19 , ARG A:23 , GLU A:110 , ASP A:254 , ASN A:255 , GLY A:383 , ASP A:384 , LEU A:385 , ARG A:388 , LYS A:423 , HOH A:499 , HOH A:565 , HOH A:589 , HOH A:590 , HOH A:592 , HOH A:593 , MG A:1002BINDING SITE FOR RESIDUE F6P A 1001
3AC3SOFTWAREASP A:254 , ASN A:255 , ASP A:292 , HOH A:589 , HOH A:590 , F6P A:1001BINDING SITE FOR RESIDUE MG A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PT1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PT1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PT1)

(-) Exons   (0, 0)

(no "Exon" information available for 3PT1)

(-) 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:464
 aligned with ARMT1_YEAST | Q04371 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:469
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         
          ARMT1_YEAST     - -MTIPGRFMTIDKGTFGEYTASTRWPIIIQNAIDDLSKHQETEKSNGTKFEQGEVIKKELKEFRQEIIDRVPLRPFTEEEIKIANVPLSFNEYLKKHPEVNWGAVEWLFSEVYLYRRVNVLFQRQCEWAKFDIFNRLKQSTFESSFYGVVELALRYENLLPQLREMKQNPGNEIDDILKVLFKEFIEISLWGNATDLSLLTNATLEDIKSIQGAKARAASESKIVVNDTEKAWEVLTKARADANSREIRVDFVLDNSGFELYADLMLAAFLLQSGLATKCIFHAKDIPYMVSDVMLKDFDILVHDLRDREFFPSGEPSTKESRALDLFAGEMEKFVSSGKIEFREDSFWTTELDYWNLDANETKYHGSILHKDLQKSNLVIFKGDLNYRKLTGDRKWPRTTKWETAIGPLATNGITSLSLRTCKADVQVALPEGLDAKLSQEWEKENPGRGSWWCCSGKWAVICFCSGI 468
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..hhhhh.......hhhhhhhhhh...eeeeehhhhhhhhhh........hhhhhhhhhhh....eeeeee...........hhhhhhhhhhhh....hhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pt1 A   0 HmTIPGRFmTIDKGTFGEYTASTRWPIIIQNAIDDLSKHQETEKSNGTKFEQGEVIKKELKEFRQEIIDRVPLRPFTEEEIKIANVPLSFNEYLKKHPEVNWGAVEWLFSEVYLYRRVNVLFQRQCEWAKFDIFNRLKQSTFESSFYGVVELALRYENLLPQLREmKQN-----DDILKVLFKEFIEISLWGNATDLSLLTNATLEDIKSIQGAKARAASESKIVVNDTEKAWEVLTKARADANSREIRVDFVLDNSGFELYADLmLAAFLLQSGLATKCIFHAKDIPYmVSDVmLKDFDILVHDLRDREFFPSGEPSTKESRALDLFAGEmEKFVSSGKIEFREDSFWTTELDYWNLDANETKYHGSILHKDLQKSNLVIFKGDLNYRKLTGDRKWPRTTKWETAIGPLATNGITSLSLRTCKADVQVALPEGLDAKLSQEWEKENPGRGSWWCCSGKWAVICFCSGI 468
                             |      |9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159     |  |-    |  179       189       199       209       219       229       239       249       259     | 269       279       289    |  299       309       319       329 |     339       349       359       369       379       389       399       409       419       429       439       449       459         
                             |      8-MSE                                                                                                                                                      165-MSE  174                                                                                        265-MSE                 289-MSE|                                  331-MSE                                                                                                                                     
                             1-MSE                                                                                                                                                                168                                                                                                                           294-MSE
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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  (0, 0)

(no "SCOP Domain" information available for 3PT1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PT1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PT1)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ARMT1_YEAST | Q04371)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0051998    protein carboxyl O-methyltransferase activity    Catalysis of the transfer of a methyl group to a carboxyl group on a protein.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.

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  3pt1
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARMT1_YEAST | Q04371: 5by0 5f13

(-) Related Entries Specified in the PDB File

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