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(-) Description

Title :  CRYSTAL STRUCTURE OF GGA1 GAT N-TERMINAL REGION IN COMPLEX WITH ARF1 GTP FORM
 
Authors :  T. Shiba, M. Kawasaki, H. Takatsu, T. Nogi, N. Matsugaki, N. Igarashi, M. Suzuki, R. Kato, K. Nakayama, S. Wakatsuki
Date :  05 Jan 03  (Deposition) - 06 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Shiba, M. Kawasaki, H. Takatsu, T. Nogi, N. Matsugaki, N. Igarashi, M. Suzuki, R. Kato, K. Nakayama, S. Wakatsuki
Molecular Mechanism Of Membrane Recruitment Of Gga By Arf In Lysosomal Protein Transport
Nat. Struct. Biol. V. 10 386 2003
PubMed-ID: 12679809  |  Reference-DOI: 10.1038/NSB920
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADP-RIBOSYLATION FACTOR 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPPROEX HT
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 18-181
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymARF1
 
Molecule 2 - ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX4T-2
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentGAT N-TERMINAL REGION
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2IOD2Ligand/IonIODIDE ION
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:31 , THR A:48 , GTP A:1001 , HOH A:1021 , HOH A:1022BINDING SITE FOR RESIDUE MG A 1002
2AC2SOFTWARETRP A:66BINDING SITE FOR RESIDUE IOD A 1
3AC3SOFTWAREARG B:180BINDING SITE FOR RESIDUE IOD B 2
4AC4SOFTWAREASP A:26 , ALA A:27 , ALA A:28 , GLY A:29 , LYS A:30 , THR A:31 , THR A:32 , THR A:45 , THR A:48 , GLY A:69 , GLY A:70 , ASN A:126 , LYS A:127 , ASP A:129 , LEU A:130 , ALA A:160 , MG A:1002 , HOH A:1015 , HOH A:1017 , HOH A:1018 , HOH A:1021 , HOH A:1022 , HOH A:1025 , HOH A:1093 , HOH A:1094 , HOH A:1095BINDING SITE FOR RESIDUE GTP A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J2J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J2J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J2J)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GATPS50909 GAT domain profile.GGA1_HUMAN171-299  1B:171-208

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENSMUST000000633472ENSMUSE00000671817chr11:103828185-103828691507ARF2_MOUSE-00--
1.3ENSMUST000000633473ENSMUSE00000226288chr11:103830393-103830559167ARF2_MOUSE1-50501A:16-50 (gaps)37
1.4ENSMUST000000633474ENSMUSE00000226282chr11:103834267-103834377111ARF2_MOUSE50-87381A:50-8738
1.6aENSMUST000000633476aENSMUSE00000107918chr11:103843008-103843132125ARF2_MOUSE87-128421A:87-12842
1.7bENSMUST000000633477bENSMUSE00000461775chr11:103844902-1038466511750ARF2_MOUSE129-181531A:129-18052

2.1aENST000003436321aENSE00001813421chr22:38004482-38004910429GGA1_HUMAN1-15150--
2.7cENST000003436327cENSE00002140158chr22:38010197-3801028185GGA1_HUMAN15-43290--
2.8aENST000003436328aENSE00001612880chr22:38012929-3801300476GGA1_HUMAN43-68260--
2.9cENST000003436329cENSE00001683976chr22:38014455-3801455399GGA1_HUMAN69-101330--
2.10fENST0000034363210fENSE00000880168chr22:38016245-38016368124GGA1_HUMAN102-143420--
2.11bENST0000034363211bENSE00000880169chr22:38016820-38016920101GGA1_HUMAN143-176341B:168-1769
2.12cENST0000034363212cENSE00000653934chr22:38017623-3801770381GGA1_HUMAN177-203271B:177-20327
2.13ENST0000034363213ENSE00000880172chr22:38019334-38019474141GGA1_HUMAN204-250471B:204-2085
2.14bENST0000034363214bENSE00000880174chr22:38019559-3801964082GGA1_HUMAN251-278280--
2.14eENST0000034363214eENSE00001286815chr22:38020976-38021083108GGA1_HUMAN278-314370--
2.15aENST0000034363215aENSE00000653938chr22:38021804-38021956153GGA1_HUMAN314-365520--
2.16ENST0000034363216ENSE00000653944chr22:38025469-3802553365GGA1_HUMAN365-386220--
2.17aENST0000034363217aENSE00000653945chr22:38026005-38026177173GGA1_HUMAN387-444580--
2.18bENST0000034363218bENSE00000653946chr22:38026910-38027106197GGA1_HUMAN444-510670--
2.19ENST0000034363219ENSE00000653947chr22:38028003-38028172170GGA1_HUMAN510-566570--
2.20ENST0000034363220ENSE00000653948chr22:38028412-38028522111GGA1_HUMAN567-603370--
2.21dENST0000034363221dENSE00001823052chr22:38028608-38029571964GGA1_HUMAN604-639360--

(-) 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:165
 aligned with ARF2_MOUSE | Q8BSL7 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:167
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       
           ARF2_MOUSE    14 GKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELTRMLAEDELRDAVLLVFVNKQDLPNAMNAAEITDKLGLHSLRQRNWYIQATCATSGDGLYEGLDWLSNQLKNQ 180
               SCOP domains d  1j2ja_ A: ADP-ribosylation factor                                                                                                                                    SCOP domains
               CATH domains 1  j2jA00 A:16-180 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--eeeeeee.....hhhhhhhhhhhh..........eeeeeeee..eeeeeeee..hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:16-50 (gaps)        ------------------------------------Exon 1.6a  PDB: A:87-128 UniProt: 87-128  Exon 1.7b  PDB: A:129-180 UniProt: 129-181           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.4  PDB: A:50-87 UniProt: 50-87 --------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1j2j A  16 G--SMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQ 180
                            |  |    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       
                            | 17                                                                                                                                                                   
                           16                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:41
 aligned with GGA1_HUMAN | Q9UJY5 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:41
                                   177       187       197       207 
           GGA1_HUMAN   168 IFEDEEKSKMLARLLKSSHPEDLRAANKLIKEMVQEDQKRM 208
               SCOP domains d1j2jb_ B:                                SCOP domains
               CATH domains 1j2jB00 B:168-208                         CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ---GAT  PDB: B:171-208 UniProt: 171-299   PROSITE
               Transcript 2 2.11b    Exon 2.12c  PDB: B:177-203 2.13  Transcript 2
                 1j2j B 168 IFEDEEKSKMLARLLKSSHPEDLRAANKLIKEMVQEDQKRM 208
                                   177       187       197       207 

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J2J)

(-) Gene Ontology  (20, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ARF2_MOUSE | Q8BSL7)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    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:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    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: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.

Chain B   (GGA1_HUMAN | Q9UJY5)
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:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    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:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    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:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GGA1_HUMAN | Q9UJY51jwf 1jwg 1na8 1naf 1nwm 1o3x 1om9 1oxz 1py1 1ujj 1ujk 1x79 2dwx 2dwy 3g2s 3g2t 3g2u 3g2v 3g2w

(-) Related Entries Specified in the PDB File

1j2h HUMAN GGA1 GAT DOMAIN
1j2i MOUSE ARF1 (DELTA17-Q71L), GTP FORM