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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SEC7 DOMAIN OF YEAST GEA2
 
Authors :  L. Renault, P. Christova, B. Guibert, S. Pasqualato, J. Cherfils
Date :  20 Jan 02  (Deposition) - 27 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sec7 Domain, Guanine Nucleotide Exchange Factor (Gef), Arf Small Gtp-Binding Proteins, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Renault, P. Christova, B. Guibert, S. Pasqualato, J. Cherfils
Mechanism Of Domain Closure Of Sec7 Domains And Role In Bfa Sensitivity.
Biochemistry V. 41 3605 2002
PubMed-ID: 11888276  |  Reference-DOI: 10.1021/BI012123H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARF GUANINE-NUCLEOTIDE EXCHANGE FACTOR 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEC7 DOMAIN (RESIDUES 570-714)
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1KU1)

(-) Sites  (0, 0)

(no "Site" information available for 1KU1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KU1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KU1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KU1)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SEC7PS50190 SEC7 domain profile.GEA2_YEAST552-754
 		  2A:558-754
B:558-754
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SEC7PS50190 SEC7 domain profile.GEA2_YEAST552-754
 		  1A:558-754
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SEC7PS50190 SEC7 domain profile.GEA2_YEAST552-754
 		  1-
B:558-754

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YEL022W1YEL022W.1V:111421-1158004380GEA2_YEAST1-145914592A:-9-759 (gaps)
B:-9-759 (gaps)		236
236

(-) 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:211
 aligned with GEA2_YEAST | P39993 from UniProtKB/Swiss-Prot  Length:1459

    Alignment length:236
                                   533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753      
           GEA2_YEAST   524 GLVSLVDDMFDHMKDIDREEFGRQKNEMEILKKRDRKTEFIECTNAFNEKPKKGIPMLIEKGFIASDSDKDIAEFLFNNNNRMNKKTIGLLLCHPDKVSLLNEYIRLFDFSGLRVDEAIRILLTKFRLPGESQQIERIIEAFSSAYCENQDYDPSKISDNAEDDISTVQPDADSVFILSYSIIMLNTDLHNPQVKEHMSFEDYSGNLKGCCNHKDFPFWYLDRIYCSIRDKEIVMP 759
               SCOP domains d1ku1a    _ A                     : ARF guanine-exchange factor 2, Gea2                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------1ku1A01 A:558-631  [code=1.10.220.20, no name defined]                    1ku1A02 A:632-759 Arf Nucleotide-binding Site Opener,domain 2                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......----.hh---------------------hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhh......hhhhh..hhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------SEC7  PDB: A:558-754 UniProt: 552-754                                                                                                                                                                      ----- PROSITE
               Transcript 1 Exon 1.1  PDB: A:-9-759 (gaps) UniProt: 1-1459 [INCOMPLETE]                                                                                                                                                                                  Transcript 1
                 1ku1 A  -9 GLVPRG----SHM---------------------DRKTEFIECTNAFNEKPKKGIPMLIEKGFIASDSDKDIAEFLFNNNNRMNKKTIGLLLCHPDKVSLLNEYIRLFDFSGLRVDEAIRILLTKFRLPGESQQIERIIEAFSSAYCENQDYDPSKISDNAEDDISTVQPDADSVFILSYSIIMLNTDLHNPQVKEHMSFEDYSGNLKGCCNHKDFPFWYLDRVYCSIRDKEIVMP 759
                                 |   -| |      -         -    |  563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753      
                                -4   -3 |                   558                                                                                                                                                                                                         
                                       -1                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with GEA2_YEAST | P39993 from UniProtKB/Swiss-Prot  Length:1459

    Alignment length:236
                                   533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753      
           GEA2_YEAST   524 GLVSLVDDMFDHMKDIDREEFGRQKNEMEILKKRDRKTEFIECTNAFNEKPKKGIPMLIEKGFIASDSDKDIAEFLFNNNNRMNKKTIGLLLCHPDKVSLLNEYIRLFDFSGLRVDEAIRILLTKFRLPGESQQIERIIEAFSSAYCENQDYDPSKISDNAEDDISTVQPDADSVFILSYSIIMLNTDLHNPQVKEHMSFEDYSGNLKGCCNHKDFPFWYLDRIYCSIRDKEIVMP 759
               SCOP domains d1ku1b    _ B                     : ARF guanine-exchange factor 2, Gea2                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------1ku1B01 B:558-631  [code=1.10.220.20, no name defined]                    1ku1B02 B:632-759 Arf Nucleotide-binding Site Opener,domain 2                                                                    CATH domains
           Pfam domains (1) ----------------------------------Sec7-1ku1B01 B:558-756                                                                                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) ----------------------------------Sec7-1ku1B02 B:558-756                                                                                                                                                                                 --- Pfam domains (2)
         Sec.struct. author ...hhh----hhh---------------------hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhh......hhhhh..hhhhhhhhhhhhhhhhhhhh........hhhhhhhh..........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------SEC7  PDB: B:558-754 UniProt: 552-754                                                                                                                                                                      ----- PROSITE
               Transcript 1 Exon 1.1  PDB: B:-9-759 (gaps) UniProt: 1-1459 [INCOMPLETE]                                                                                                                                                                                  Transcript 1
                 1ku1 B  -9 GLVPRG----SHM---------------------DRKTEFIECTNAFNEKPKKGIPMLIEKGFIASDSDKDIAEFLFNNNNRMNKKTIGLLLCHPDKVSLLNEYIRLFDFSGLRVDEAIRILLTKFRLPGESQQIERIIEAFSSAYCENQDYDPSKISDNAEDDISTVQPDADSVFILSYSIIMLNTDLHNPQVKEHMSFEDYSGNLKGCCNHKDFPFWYLDRVYCSIRDKEIVMP 759
                                 |   -| |      -         -    |  563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753      
                                -4   -3 |                   558                                                                                                                                                                                                         
                                       -1
   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  (2, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Sec7] (12)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GEA2_YEAST | P39993)
molecular function
    GO:0005086    ARF guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with the GTPase ARF. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0006891    intra-Golgi vesicle-mediated transport    The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
    GO:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0032012    regulation of ARF protein signal transduction    Any process that modulates the frequency, rate or extent of ARF protein signal transduction.
    GO:0006890    retrograde vesicle-mediated transport, Golgi to ER    The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
    GO:0033363    secretory granule organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion.
cellular component
    GO:0000137    Golgi cis cisterna    The Golgi cisterna closest to the endoplasmic reticulum; the first processing compartment through which proteins pass after export from the ER.
    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:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1bc9 1BC9 CONTAINS THE SEC7 DOMAIN OF CYTOHESIN-1/B2-1
1pbv 1PBV CONTAINS THE SEC7 DOMAIN OF THE EXCHANGE FACTOR ARNO