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(-) Description

Title :  CRYSTAL STRUCTURE OF IIGP1: A PARADIGM FOR INTERFERON INDUCIBLE P47 RESISTANCE GTPASES
 
Authors :  A. Ghosh, R. Uthaiah, J. Howard, C. Herrmann, E. Wolf
Date :  17 Jun 04  (Deposition) - 21 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gtpase, Interferon Gamma, Crystal Structure, Dimer, Immunology, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ghosh, R. Uthaiah, J. Howard, C. Herrmann, E. Wolf
Crystal Structure Of Iigp1; A Paradigm For Interferon-Inducible P47 Resistance Gtpases
Mol. Cell V. 15 727 2004
PubMed-ID: 15350217  |  Reference-DOI: 10.1016/J.MOLCEL.2004.07.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERFERON-INDUCIBLE GTPASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: IIGP1
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: IIGP1

 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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:79 , SER B:80 , GLY B:81 , LYS B:82 , SER B:83 , SER B:84 , THR B:102 , LYS B:184 , HOH B:2269BINDING SITE FOR RESIDUE SO4 B 1000
2AC2SOFTWARESER B:35 , GLU B:64 , ILE B:253 , TYR B:254 , HOH B:2073 , HOH B:2257BINDING SITE FOR RESIDUE MES B 2000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_IRGPS51716 IRG-type guanine nucleotide-binding (G) domain profile.IIGP1_MOUSE68-250
 
  2A:68-250
B:68-250
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_IRGPS51716 IRG-type guanine nucleotide-binding (G) domain profile.IIGP1_MOUSE68-250
 
  1A:68-250
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_IRGPS51716 IRG-type guanine nucleotide-binding (G) domain profile.IIGP1_MOUSE68-250
 
  1-
B:68-250

(-) Exons   (0, 0)

(no "Exon" information available for 1TQD)

(-) 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:385
 aligned with IIGP1_MOUSE | Q9QZ85 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:400
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413
          IIGP1_MOUSE    14 NDLPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPNTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISMMKKEFYFVRTKVDSDITNEADGKPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVSLPNITDSVIEKKRQFLKQRIWLEGFAADLVNIIPSLTFLLDSDLETLKKSMKFYRTVFGVDETSLQRLARDWEIEVDQVEAMIKSPAVFKPTDEETIQERLSRYIQEFCLANGYLLPKNSFLKEIFYLKYYFLDMVTEDAKTLLKEICLRN 413
               SCOP domains d1tqda_ A: Interferon-inducible GTPase                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.............---....eeee......eeeee..hhhhh..hhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh..eeeeee.hhhhh.------------...hhhhhhhhhhhhhhhh......eee.........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------G_IRG  PDB: A:68-250 UniProt: 68-250                                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tqd A  14 NDLPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGV---TMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISMMKKEFYFVRTKVDSDI------------KEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVSLPNITDSVIEKKRQFLKQRIWLEGFAADLVNIIPSLTFLLDSDLETLKKSMKFYRTVFGVDETSLQRLARDWEIEVDQVEAMIKSPAVFKPTDEETIQERLSRYIQEFCLANGYLLPKNSFLKEIFYLKYYFLDMVTEDAKTLLKEICLRN 413
                                    23        33        43        53        63        73        83        93       103|   |  113       123       133       143       153       163       173       183     |   -       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413
                                                                                                                    104 108                                                                              189          202                                                                                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:379
 aligned with IIGP1_MOUSE | Q9QZ85 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:400
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413
          IIGP1_MOUSE    14 NDLPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPNTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISMMKKEFYFVRTKVDSDITNEADGKPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVSLPNITDSVIEKKRQFLKQRIWLEGFAADLVNIIPSLTFLLDSDLETLKKSMKFYRTVFGVDETSLQRLARDWEIEVDQVEAMIKSPAVFKPTDEETIQERLSRYIQEFCLANGYLLPKNSFLKEIFYLKYYFLDMVTEDAKTLLKEICLRN 413
               SCOP domains d1tqdb_ B: Interferon-inducible GTPase                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------IIGP-1tqdB01 B:35-409                                                                                                                                                                                                                                                                                                                                                                  ---- Pfam domains (1)
           Pfam domains (2) ---------------------IIGP-1tqdB02 B:35-409                                                                                                                                                                                                                                                                                                                                                                  ---- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhh...........-----....eeee......eeeeee...-------.hhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhh.---------..hhhhhhhhhhhhhhhh.......eee.........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------G_IRG  PDB: B:68-250 UniProt: 68-250                                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tqd B  14 NDLPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKT-----TMERHPYKHPNIPNVVFWDLPGI-------DTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISMMKKEFYFVRTKVDSDITNE---------KEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVSLPNITDSVIEKKRQFLKQRIWLEGFAADLVNIIPSLTFLLDSDLETLKKSMKFYRTVFGVDETSLQRLARDWEIEVDQVEAMIKSPAVFKPTDEETIQERLSRYIQEFCLANGYLLPKNSFLKEIFYLKYYFLDMVTEDAKTLLKEICLRN 413
                                    23        33        43        53        63        73        83        93        |-    |  113       123      |  -    |  143       153       163       173       183        |-       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413
                                                                                                                  102   108                   130     138                                                   192       202                                                                                                                                                                                                                   

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1TQD)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IIGP1_MOUSE | Q9QZ85)
molecular function
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0035458    cellular response to interferon-beta    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 an interferon-beta stimulus. Interferon-beta is a type I interferon.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0042832    defense response to protozoan    Reactions triggered in response to the presence of a protozoan that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
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:0032580    Golgi cisterna membrane    The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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:0020005    symbiont-containing vacuole membrane    The lipid bilayer surrounding a symbiont-containing vacuole, derived from both the host and symbiont.

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  IIGP1_MOUSE | Q9QZ85
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 Related Entries

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

UniProtKB/Swiss-Prot
        IIGP1_MOUSE | Q9QZ85: 1tpz 1tq2 1tq4 1tq6 4lv5 4lv8 5fph

(-) Related Entries Specified in the PDB File

1dg3
1f5n
1tpz THE SAME PROTEIN WITH GDP
1tq2 THE SAME PROTEIN WITH GNP
1tq4 THE SAME PROTEIN, K48A MUTANT WITH GDP
1tq6 THE SAME PROTEIN, M173A MUTANT WITH GNP