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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST PROTEASOME INTERACTING PROTEIN
 
Authors :  K. Takagi, S. Kim, K. Kato, K. Tanaka, Y. Saeki, T. Mizushima
Date :  01 Dec 11  (Deposition) - 22 Feb 12  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Heat Repeat, Rpt1, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Takagi, S. Kim, H. Yukii, M. Ueno, R. Morishita, Y. Endo, K. Kato, K. Tanaka, Y. Saeki, T. Mizushima
Structural Basis For Specific Recognition Of Rpt1, An Atpas Subunit Of The 26S Proteasome, By A Proteasome-Dedicated Chaperone Hsm3
J. Biol. Chem. V. 287 12172 2012
PubMed-ID: 22334676  |  Reference-DOI: 10.1074/JBC.M112.345876

(-) Compounds

Molecule 1 - DNA MISMATCH REPAIR PROTEIN HSM3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HSM3, YBR1740, YBR272C
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: ENHANCED SPONTANEOUS MUTABILITY PROTEIN 3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3VLD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:124 -Pro A:125
2Val B:9 -Glu B:10
3Gln B:124 -Pro B:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VLD)

(-) Sequences/Alignments

Asymmetric 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:457
 aligned with HSM3_YEAST | P38348 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:457
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       
           HSM3_YEAST     9 VENLLTQLENELNEDNLPEDINTLLRKCSLNLVTVVSLPDMDVKPLLATIKRFLTSNVSYDSLNYDYLLDVVDKLVPMADFDDVLEVYSAEDLVKALRSEIDPLKVAACRVIENSQPKGLFATSNIIDILLDILFDEKVENDKLITAIEKALERLSTDELIRRRLFDNNLPYLVSVKGRMETVSFVRLIDFLTIEFQFISGPEFKDIIFCFTKEEILKSVEDILVFIELVNYYTKFLLEIRNQDKYWALRHVKKILPVFAQLFEDTENYPDVRAFSTNCLLQLFAEVSRIEEDEYSLFKTMDKDSLKIGSEAKLITEWLELINPQYLVKYHKDVVENYFHVSGYSIGMLRNLSADEECFNAIRNKFSAEIVLRLPYLEQMQVVETLTRYEYTSKFLLNEMPKVMGSLIGDGSAGAIIDLETVHYRNSALRNLLDKGEEKLSVWYEPLLREYSKAVNG 465
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vld A   9 VENLLTQLENELNEDNLPEDINTLLRKCSLNLVTVVSLPDmDVKPLLATIKRFLTSNVSYDSLNYDYLLDVVDKLVPmADFDDVLEVYSAEDLVKALRSEIDPLKVAACRVIENSQPKGLFATSNIIDILLDILFDEKVENDKLITAIEKALERLSTDELIRRRLFDNNLPYLVSVKGRmETVSFVRLIDFLTIEFQFISGPEFKDIIFCFTKEEILKSVEDILVFIELVNYYTKFLLEIRNQDKYWALRHVKKILPVFAQLFEDTENYPDVRAFSTNCLLQLFAEVSRIEEDEYSLFKTmDKDSLKIGSEAKLITEWLELINPQYLVKYHKDVVENYFHVSGYSIGmLRNLSADEECFNAIRNKFSAEIVLRLPYLEQmQVVETLTRYEYTSKFLLNEmPKVmGSLIGDGSAGAIIDLETVHYRNSALRNLLDKGEEKLSVWYEPLLREYSKAVNG 465
                                    18        28        38        48|       58        68        78       |88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308|      318       328       338       348       358       368       378       388       398       408   |   418       428       438       448       458       
                                                                   49-MSE                               86-MSE                                                                                               188-MSE                                                                                                                  309-MSE                                        356-MSE                         388-MSE             408-MSE                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                             412-MSE                                                 


Chain B from PDB  Type:PROTEIN  Length:457
 aligned with HSM3_YEAST | P38348 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:457
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       
           HSM3_YEAST     9 VENLLTQLENELNEDNLPEDINTLLRKCSLNLVTVVSLPDMDVKPLLATIKRFLTSNVSYDSLNYDYLLDVVDKLVPMADFDDVLEVYSAEDLVKALRSEIDPLKVAACRVIENSQPKGLFATSNIIDILLDILFDEKVENDKLITAIEKALERLSTDELIRRRLFDNNLPYLVSVKGRMETVSFVRLIDFLTIEFQFISGPEFKDIIFCFTKEEILKSVEDILVFIELVNYYTKFLLEIRNQDKYWALRHVKKILPVFAQLFEDTENYPDVRAFSTNCLLQLFAEVSRIEEDEYSLFKTMDKDSLKIGSEAKLITEWLELINPQYLVKYHKDVVENYFHVSGYSIGMLRNLSADEECFNAIRNKFSAEIVLRLPYLEQMQVVETLTRYEYTSKFLLNEMPKVMGSLIGDGSAGAIIDLETVHYRNSALRNLLDKGEEKLSVWYEPLLREYSKAVNG 465
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vld B   9 VENLLTQLENELNEDNLPEDINTLLRKCSLNLVTVVSLPDmDVKPLLATIKRFLTSNVSYDSLNYDYLLDVVDKLVPmADFDDVLEVYSAEDLVKALRSEIDPLKVAACRVIENSQPKGLFATSNIIDILLDILFDEKVENDKLITAIEKALERLSTDELIRRRLFDNNLPYLVSVKGRmETVSFVRLIDFLTIEFQFISGPEFKDIIFCFTKEEILKSVEDILVFIELVNYYTKFLLEIRNQDKYWALRHVKKILPVFAQLFEDTENYPDVRAFSTNCLLQLFAEVSRIEEDEYSLFKTmDKDSLKIGSEAKLITEWLELINPQYLVKYHKDVVENYFHVSGYSIGmLRNLSADEECFNAIRNKFSAEIVLRLPYLEQmQVVETLTRYEYTSKFLLNEmPKVmGSLIGDGSAGAIIDLETVHYRNSALRNLLDKGEEKLSVWYEPLLREYSKAVNG 465
                                    18        28        38        48|       58        68        78       |88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308|      318       328       338       348       358       368       378       388       398       408   |   418       428       438       448       458       
                                                                   49-MSE                               86-MSE                                                                                               188-MSE                                                                                                                  309-MSE                                        356-MSE                         388-MSE             408-MSE                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                             412-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 3VLD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HSM3_YEAST | P38348)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    GO:0070682    proteasome regulatory particle assembly    The aggregation, arrangement and bonding together of a mature, active proteasome regulatory particle complex.
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.
    GO:0008540    proteasome regulatory particle, base subcomplex    The subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HSM3_YEAST | P38348: 3vle 3vlf 4a3t 4a3v 4fp7 4jpo

(-) Related Entries Specified in the PDB File

3vle 3vlf