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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST FIS1 COMPLEXED WITH A FRAGMENT OF YEAST CAF4
 
Authors :  Y. Zhang, D. C. Chan
Date :  02 May 07  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Tpr Domain, Protein-Protein Complex, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, D. C. Chan
Structural Basis For Recruitment Of Mitochondrial Fission Complexes By Fis1.
Proc. Natl. Acad. Sci. Usa V. 104 18526 2007
PubMed-ID: 17998537  |  Reference-DOI: 10.1073/PNAS.0706441104

(-) Compounds

Molecule 1 - MITOCHONDRIA FISSION 1 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBB75
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CYTOPLASMIC PORTION
    Gene: FIS1, MDV2
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: MITOCHONDRIAL DIVISION PROTEIN 2
 
Molecule 2 - WD REPEAT PROTEIN YKR036C
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Gene: CAF4
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1AU2Ligand/IonGOLD ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:303 , HOH B:312BINDING SITE FOR RESIDUE AU B 301
2AC2SOFTWAREHOH B:382BINDING SITE FOR RESIDUE AU D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PQR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn D:116 -Gly D:117
2Ala D:118 -Ala D:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PQR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PQR)

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIL065C1YIL065C.1IX:241772-241305468FIS1_YEAST1-1551552A:5-102
B:5-128		98
124
2.1YKR036C1YKR036C.1XI:510275-5083441932CAF4_YEAST1-6436432C:97-140 (gaps)
D:94-138		44
45

(-) 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:98
 aligned with FIS1_YEAST | P40515 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:98
                                    14        24        34        44        54        64        74        84        94        
           FIS1_YEAST     5 DFWPTLKDAYEPLYPQQLEILRQQVVSEGGPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDT 102
               SCOP domains d2pqra_ A: Mitochondria fission protein Fis1                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-102 UniProt: 1-155 [INCOMPLETE]                                                 Transcript 1
                 2pqr A   5 DFWPTLKDAYEPLYPQQLEILRQQVVSEGGPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDT 102
                                    14        24        34        44        54        64        74        84        94        


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with FIS1_YEAST | P40515 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:124
                                    14        24        34        44        54        64        74        84        94       104       114       124    
           FIS1_YEAST     5 DFWPTLKDAYEPLYPQQLEILRQQVVSEGGPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQVGALKSMVEDKIQKET 128
               SCOP domains d2pqrb_ B: Mitochondria fission protein Fis1                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:5-128 UniProt: 1-155 [INCOMPLETE]                                                                           Transcript 1
                 2pqr B   5 DFWPTLKDAYEPLYPQQLEILRQQVVSEGGPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQVGALKSMVEDKIQKET 128
                                    14        24        34        44        54        64        74        84        94       104       114       124    


Chain C from PDB  Type:PROTEIN  Length:40
 aligned with CAF4_YEAST | P36130 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:44
                                    90       100       110       120    
           CAF4_YEAST    81 SATTFRILAHLDEQRYPLPNGAAEKNLPSLFEGFKATVSIIQQR 124
               SCOP domains -------------------------------------------- SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..........----.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: C:97-140 (gaps) [INCOMPLETE]  Transcript 2
                 2pqr C  97 SATTFRILAHLDEQRYPLP----EKNLPSLFEGFKATVSIIQQR 140
                                   106        |-   |   126       136    
                                            115  120                    


Chain D from PDB  Type:PROTEIN  Length:45
 aligned with CAF4_YEAST | P36130 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:45
                                    87        97       107       117     
           CAF4_YEAST    78 YADSATTFRILAHLDEQRYPLPNGAAEKNLPSLFEGFKATVSIIQ 122
               SCOP domains --------------------------------------------- SCOP domains
               CATH domains --------------------------------------------- CATH domains
           Pfam domains (1) DUF3249-2pqrD01 D:94-138                      Pfam domains (1)
           Pfam domains (2) DUF3249-2pqrD02 D:94-138                      Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhh...................hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: D:94-138 UniProt: 1-643        Transcript 2
                 2pqr D  94 YADSATTFRILAHLDEQRYPLPNGAAEKNLPSLFEGFKATVSIIQ 138
                                   103       113       123       133
   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  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PQR)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF3249] (1)

(-) Gene Ontology  (14, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FIS1_YEAST | P40515)
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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0001300    chronological cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs when the cell is in a non-dividing, or quiescent, state.
    GO:0000266    mitochondrial fission    The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
    GO:0016559    peroxisome fission    The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments.
    GO:0007031    peroxisome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
    GO:0090141    positive regulation of mitochondrial fission    Any process that increases the rate, frequency or extent of mitochondrial fission. Mitochondrial fission is the division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

Chain C,D   (CAF4_YEAST | P36130)
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:0000266    mitochondrial fission    The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
    GO:0016559    peroxisome fission    The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
cellular component
    GO:0030014    CCR4-NOT complex    The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FIS1_YEAST | P40515: 1y8m 2pqn 3o48 3uux

(-) Related Entries Specified in the PDB File

2pqn YEAST FIS1 COMPLEXED WITH A FRAGMENT OF YEAST MDV1