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(-) Description

Title :  CRYSTAL STRUCTURE OF GAE DOMAIN OF GGA2P FROM SACCHAROMYCES CEREVISIAE
 
Authors :  P. Fang, J. Wang, X. Li, L. Niu, M. Teng
Date :  21 Apr 10  (Deposition) - 08 Sep 10  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A,B  (1x)
Biol. Unit 5:  C  (2x)
Keywords :  Ig-Like, Beta Sandwich, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Fang, X. Li, J. Wang, L. Niu, M. Teng
Structural Basis For The Specificity Of The Gae Domain Of Ygga2 For Its Accessory Proteins Ent3 And Ent5
Biochemistry V. 49 7949 2010
PubMed-ID: 20704189  |  Reference-DOI: 10.1021/BI1010255

(-) Compounds

Molecule 1 - ADP-RIBOSYLATION FACTOR-BINDING PROTEIN GGA2
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GAE DOMAIN
    Gene: GGA2
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: GOLGI-LOCALIZED, GAMMA EAR-CONTAINING, ARF-BINDING PROTEIN 2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (1x): AB 
Biological Unit 5 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2MLY9Mod. Amino AcidN-DIMETHYL-LYSINE
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MLY3Mod. Amino AcidN-DIMETHYL-LYSINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MLY3Mod. Amino AcidN-DIMETHYL-LYSINE
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLY3Mod. Amino AcidN-DIMETHYL-LYSINE
3SO41Ligand/IonSULFATE ION
Biological Unit 4 (3, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MLY6Mod. Amino AcidN-DIMETHYL-LYSINE
3SO42Ligand/IonSULFATE ION
Biological Unit 5 (3, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MLY6Mod. Amino AcidN-DIMETHYL-LYSINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:305 , HOH A:319 , HOH A:323 , MLY A:560 , THR B:572 , GLN B:573BINDING SITE FOR RESIDUE SO4 A 2
2AC2SOFTWAREHOH A:14 , HOH A:44 , HOH A:72 , ASN A:511 , LEU A:515 , LEU A:516 , TYR A:567 , SER A:568 , GLN A:573 , HOH A:588BINDING SITE FOR RESIDUE GOL A 1
3AC3SOFTWARESER A:506 , SER A:507 , PRO A:508 , ILE A:535 , GLY A:536 , HOH A:593 , HOH B:93 , PRO B:508 , PHE B:533 , MLY C:525BINDING SITE FOR RESIDUE GOL A 586
4AC4SOFTWARETHR A:572 , GLN A:573 , HOH B:131 , HOH B:256 , HOH B:417 , MLY B:560BINDING SITE FOR RESIDUE SO4 B 1
5AC5SOFTWAREHOH B:270 , ALA B:517 , VAL B:518 , PRO B:519 , MLY B:560 , LYS B:562BINDING SITE FOR RESIDUE GOL B 3
6AC6SOFTWAREHOH B:135 , ASN B:511 , VAL B:513 , TYR B:567 , SER B:568 , GLN B:573 , HOH B:586 , HOH C:314 , LEU C:516BINDING SITE FOR RESIDUE GOL B 4
7AC7SOFTWAREHOH C:276 , THR C:572 , GLN C:573 , HOH C:592BINDING SITE FOR RESIDUE SO4 C 3
8AC8SOFTWARELEU B:515 , LEU B:516 , ALA B:517 , HOH C:39 , HOH C:84 , HOH C:86 , ASN C:511 , VAL C:513 , TYR C:567 , GLN C:573BINDING SITE FOR RESIDUE GOL C 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MNM)

(-) 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:112
 aligned with GGA2_YEAST | P38817 from UniProtKB/Swiss-Prot  Length:585

    Alignment length:115
                                   480       490       500       510       520       530       540       550       560       570       580     
           GGA2_YEAST   471 ARTLVNQSPNLKIEFEISRESNSVIRIKSFFTNLSSSPISNLVFLLAVPKSMSLKLQPQSSNFMIGNAKDGISQEGTIENAPANPSKALKVKWKVNYSVNSTQAEETAVFTLPNV 585
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeeeeee.....eeeeeeeee.....eeeeeeeee.....eeee...............eeeeeeee.....---..eeeeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnm A 471 ARTLVNQSPNLKIEFEISRESNSVIRIkSFFTNLSSSPISNLVFLLAVPKSMSLkLQPQSSNFMIGNAKDGISQEGTIENAPAN---ALkVKWKVNYSVNSTQAEETAVFTLPNV 585
                                   480       490       500       510       520    |  530       540       550   |   560       570       580     
                                                     498-MLY                    525-MLY                      554 558 |                         
                                                                                                                   560-MLY                     


Chain B from PDB  Type:PROTEIN  Length:112
 aligned with GGA2_YEAST | P38817 from UniProtKB/Swiss-Prot  Length:585

    Alignment length:115
                                   480       490       500       510       520       530       540       550       560       570       580     
           GGA2_YEAST   471 ARTLVNQSPNLKIEFEISRESNSVIRIKSFFTNLSSSPISNLVFLLAVPKSMSLKLQPQSSNFMIGNAKDGISQEGTIENAPANPSKALKVKWKVNYSVNSTQAEETAVFTLPNV 585
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeeeeeeee..eeeeeeeeee......eeeeeeee.....eeee...............eeeeeeee.....---..eeeeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnm B 471 ARTLVNQSPNLKIEFEISRESNSVIRIkSFFTNLSSSPISNLVFLLAVPKSMSLkLQPQSSNFMIGNAKDGISQEGTIENAPAN---ALkVKWKVNYSVNSTQAEETAVFTLPNV 585
                                   480       490       500       510       520    |  530       540       550   |   560       570       580     
                                                     498-MLY                    525-MLY                      554 558 |                         
                                                                                                                   560-MLY                     


Chain C from PDB  Type:PROTEIN  Length:110
 aligned with GGA2_YEAST | P38817 from UniProtKB/Swiss-Prot  Length:585

    Alignment length:116
                                   479       489       499       509       519       529       539       549       559       569       579      
           GGA2_YEAST   470 PARTLVNQSPNLKIEFEISRESNSVIRIKSFFTNLSSSPISNLVFLLAVPKSMSLKLQPQSSNFMIGNAKDGISQEGTIENAPANPSKALKVKWKVNYSVNSTQAEETAVFTLPNV 585
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Alpha_adaptinC2-3mnmC01 C:471-583                                                                                -- Pfam domains (1)
           Pfam domains (2) -Alpha_adaptinC2-3mnmC02 C:471-583                                                                                -- Pfam domains (2)
           Pfam domains (3) -Alpha_adaptinC2-3mnmC03 C:471-583                                                                                -- Pfam domains (3)
         Sec.struct. author ..eeeeee...eeeeeeeee.....eeeeeeeee.....eeeeeeeee.....eeee...............eeeeeeee..------.eeeeeeeeeee..eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnm C 470 PARTLVNQSPNLKIEFEISRESNSVIRIkSFFTNLSSSPISNLVFLLAVPKSMSLkLQPQSSNFMIGNAKDGISQEGTIENA------ALkVKWKVNYSVNSTQAEETAVFTLPNV 585
                                   479       489       499       509       519     | 529       539       549 |     559|      569       579      
                                                      498-MLY                    525-MLY                   551    558 |                         
                                                                                                                    560-MLY
   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 3MNM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: E-set (290)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (GGA2_YEAST | P38817)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
    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).
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0006895    Golgi to endosome transport    The directed movement of substances from the Golgi to early sorting endosomes. Clathrin vesicles transport substances from the trans-Golgi to endosomes.
    GO:0006896    Golgi to vacuole transport    The directed movement of substances from the Golgi to the vacuole.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0043328    protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway    The process of directing proteins towards the vacuole that contributes to protein catabolism via the multivesicular body (MVB) pathway.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0030131    clathrin adaptor complex    A membrane coat adaptor complex that links clathrin to a membrane.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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