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(-) Description

Title :  CRYSTAL STRUCTURE OF MITOCHONDRIAL HAD-LIKE PHOSPHATASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  B. Nocek, E. Evdokimova, K. Kuznetsova, A. Iakunine, A. Savchenko, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  20 Oct 09  (Deposition) - 24 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Had-Like, Mitochondral Protein, Psi, Mcsg, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Phosphoprotein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, E. Evdokimova, K. Kuznetsova, A. Iakunine, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of Mitochondrial Had-Like Phosphatase Fro Saccharomyces Cerevisiae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN YKR070W
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PMAGIC
    Gene: YKR070W
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:19 , ILE A:20 , ASP A:21 , THR A:52 , ASN A:53 , GLY A:54 , LYS A:246 , MG A:355 , HOH A:893 , HOH A:894 , HOH A:895BINDING SITE FOR RESIDUE PO4 A 353
2AC2SOFTWARELEU A:225 , ARG A:228 , HOH A:479 , HOH A:544 , HOH A:684 , HOH A:862 , ARG B:229BINDING SITE FOR RESIDUE PO4 A 354
3AC3SOFTWAREASP A:19 , ASP A:21 , ASP A:298 , PO4 A:353 , HOH A:893 , HOH A:894BINDING SITE FOR RESIDUE MG A 355
4AC4SOFTWAREASP B:19 , ASP B:21 , ASP B:298 , PO4 B:354 , HOH B:891 , HOH B:892BINDING SITE FOR RESIDUE MG B 353
5AC5SOFTWAREASP B:19 , ILE B:20 , ASP B:21 , THR B:52 , ASN B:53 , GLY B:54 , LYS B:246 , MG B:353 , HOH B:454 , HOH B:548 , HOH B:891 , HOH B:892BINDING SITE FOR RESIDUE PO4 B 354
6AC6SOFTWAREARG A:229 , LEU B:225 , ARG B:228 , HOH B:447 , HOH B:602 , HOH B:686 , HOH B:787BINDING SITE FOR RESIDUE PO4 B 355
7AC7SOFTWAREGLY A:134 , GLN A:139 , GLY B:134 , GLN B:139 , HOH B:362 , HOH B:429BINDING SITE FOR RESIDUE MG B 356

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KC2)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:246 -Pro A:247
2Ser A:288 -Pro A:289
3Lys B:246 -Pro B:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KC2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KC2)

(-) Exons   (0, 0)

(no "Exon" information available for 3KC2)

(-) 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:327
 aligned with YK50_YEAST | P36151 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:341
                                    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       331       341       351 
           YK50_YEAST    12 KKIAFAFDIDGVLFRGKKPIAGASDALKLLNRNKIPYILLTNGGGFSERARTEFISSKLDVDVSPLQIIQSHTPYKSLVNKYSRILAVGTPSVRGVAEGYGFQDVVHQTDIVRYNRDIAPFSGLSDEQVMEYSRDIPDLTTKKFDAVLVFNDPHDWAADIQIISDAINSENGMLNTLRNEKSGKPSIPIYFSNQDLLWANPYKLNRFGQGAFRLLVRRLYLELNGEPLQDYTLGKPTKLTYDFAHHVLIDWEKRLSGKIGQSVKQKLPLLGTKPSTSPFHAVFMVGDNPASDIIGAQNYGWNSCLVKTGVYNEGDDLKECKPTLIVNDVFDAVTKTLEKYA 352
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......ee..ee..hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhh...hhh.ee..hhhhhhhh....eeeee...hhhhhhhhhh..eeeehhhhhhhhhhhh.....hhhhhhhhh............eeee.....hhhhhhhhhhhhhh....................eee.....ee.......eehhhhhhhhhhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhh--------------.........eeeeee....hhhhhhhhhh.eeee..................ee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kc2 A  12 KKIAFAFDIDGVLFRGKKPIAGASDALKLLNRNKIPYILLTNGGGFSERARTEFISSKLDVDVSPLQIIQSHTPYKSLVNKYSRILAVGTPSVRGVAEGYGFQDVVHQTDIVRYNRDIAPFSGLSDEQVmEYSRDIPDLTTKKFDAVLVFNDPHDWAADIQIISDAINSENGmLNTLRNEKSGKPSIPIYFSNQDLLWANPYKLNRFGQGAFRLLVRRLYLELNGEPLQDYTLGKPTKLTYDFAHHVLIDWEKRLSG--------------TKPSTSPFHAVFmVGDNPASDIIGAQNYGWNSCLVKTGVYNEGDDLKECKPTLIVNDVFDAVTKTLEKYA 352
                                    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      |  -         - |     291   |   301       311       321       331       341       351 
                                                                                                                                                           141-MSE                                    184-MSE                                                                             268            283         295-MSE                                                     


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with YK50_YEAST | P36151 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:340
                                    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       342       352
           YK50_YEAST    13 KIAFAFDIDGVLFRGKKPIAGASDALKLLNRNKIPYILLTNGGGFSERARTEFISSKLDVDVSPLQIIQSHTPYKSLVNKYSRILAVGTPSVRGVAEGYGFQDVVHQTDIVRYNRDIAPFSGLSDEQVMEYSRDIPDLTTKKFDAVLVFNDPHDWAADIQIISDAINSENGMLNTLRNEKSGKPSIPIYFSNQDLLWANPYKLNRFGQGAFRLLVRRLYLELNGEPLQDYTLGKPTKLTYDFAHHVLIDWEKRLSGKIGQSVKQKLPLLGTKPSTSPFHAVFMVGDNPASDIIGAQNYGWNSCLVKTGVYNEGDDLKECKPTLIVNDVFDAVTKTLEKYA 352
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......ee..ee..hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhh...hhh.ee..hhhhhhhh....eeeee...hhhhhhhhhh..eeeehhhhhhhhhhhh.....hhhhhhhhh............eeee.....hhhhhhhhhhhhhh....................eee.....ee.......eehhhhhhhhhhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhh---------------------...eeeeee....hhhhhhhhhh.eeee..................ee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kc2 B  13 KIAFAFDIDGVLFRGKKPIAGASDALKLLNRNKIPYILLTNGGGFSERARTEFISSKLDVDVSPLQIIQSHTPYKSLVNKYSRILAVGTPSVRGVAEGYGFQDVVHQTDIVRYNRDIAPFSGLSDEQVmEYSRDIPDLTTKKFDAVLVFNDPHDWAADIQIISDAINSENGmLNTLRNEKSGKPSIPIYFSNQDLLWANPYKLNRFGQGAFRLLVRRLYLELNGEPLQDYTLGKPTKLTYDFAHHVLIDWEKRLS---------------------PFHAVFmVGDNPASDIIGAQNYGWNSCLVKTGVYNEGDDLKECKPTLIVNDVFDAVTKTLEKYA 352
                                    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    |    -         -      |292  |    302       312       322       332       342       352
                                                                                                                                                          141-MSE                                    184-MSE                                                                            267                   289     |                                                         
                                                                                                                                                                                                                                                                                                                    295-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 3KC2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KC2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KC2)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YK50_YEAST | P36151)
molecular function
    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.
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:0046474    glycerophospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.

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 Related Entries

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        YK50_YEAST | P36151: 3rf6

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