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(-) Description

Title :  CRYSTAL-STRUCTURE OF THE N-TERMINAL LARGE GTPASE DOMAIN OF HUMAN GUANYLATE BINDING PROTEIN 1 (HGBP1) IN COMPLEX WITH GMP/ALF4
 
Authors :  A. Ghosh, G. J. K. Praefcke, L. Renault, A. Wittinghofer, C. Herrmann
Date :  10 Oct 05  (Deposition) - 07 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein- Guanine Nucleotide Complex, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ghosh, G. J. Praefcke, L. Renault, A. Wittinghofer, C. Herrmann
How Guanylate-Binding Proteins Achieve Assembly-Stimulated Processive Cleavage Of Gtp To Gmp.
Nature V. 440 101 2006
PubMed-ID: 16511497  |  Reference-DOI: 10.1038/NATURE04510
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPQE9
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL LARGE GTPASE DOMAIN
    GeneGBP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGTP-BINDING PROTEIN 1, GUANINE NUCLEOTIDE-BINDING PROTEIN 1, HUGBP-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2ALF2Ligand/IonTETRAFLUOROALUMINATE ION
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:52 , THR A:75 , 5GP A:593 , ALF A:594 , HOH A:633 , HOH A:647BINDING SITE FOR RESIDUE MG A 595
2AC2SOFTWARESER B:52 , THR B:75 , 5GP B:593 , ALF B:594 , HOH B:649 , HOH B:671BINDING SITE FOR RESIDUE MG B 595
3AC3SOFTWARETYR A:47 , ARG A:48 , LYS A:51 , SER A:73 , HIS A:74 , THR A:75 , THR A:98 , GLY A:100 , 5GP A:593 , MG A:595 , HOH A:602 , HOH A:633BINDING SITE FOR RESIDUE ALF A 594
4AC4SOFTWARETYR B:47 , ARG B:48 , LYS B:51 , SER B:73 , HIS B:74 , THR B:75 , GLY B:100 , 5GP B:593 , MG B:595 , HOH B:599 , HOH B:649 , HOH B:671BINDING SITE FOR RESIDUE ALF B 594
5AC5SOFTWAREARG A:48 , THR A:49 , GLY A:50 , LYS A:51 , SER A:52 , TYR A:53 , GLY A:68 , ARG A:183 , ASP A:184 , PRO A:241 , LEU A:247 , LEU A:250 , ALF A:594 , MG A:595 , HOH A:603 , HOH A:619 , LEU B:187BINDING SITE FOR RESIDUE 5GP A 593
6AC6SOFTWAREARG B:48 , THR B:49 , GLY B:50 , LYS B:51 , SER B:52 , TYR B:53 , GLY B:68 , ARG B:183 , ASP B:184 , PRO B:241 , LEU B:247 , LEU B:250 , ALF B:594 , MG B:595 , HOH B:623 , HOH B:670 , HOH B:671BINDING SITE FOR RESIDUE 5GP B 593

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B8W)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:156 -Ser B:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033950I78VGBP1_HUMANPolymorphism1048401A/BI78V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_GB1_RHD3PS51715 GB1/RHD3-type guanine nucleotide-binding (G) domain profile.GBP1_HUMAN35-278
 
  2A:35-278
B:35-278

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003704731aENSE00001452810chr1:89531043-89530843201GBP1_HUMAN-00--
1.2aENST000003704732aENSE00001452808chr1:89528936-89528728209GBP1_HUMAN1-64642A:6-64
B:6-64
59
59
1.5aENST000003704735aENSE00001676167chr1:89526007-89525880128GBP1_HUMAN64-106432A:64-106
B:64-106
43
43
1.6bENST000003704736bENSE00001681134chr1:89525109-89525000110GBP1_HUMAN107-143372A:107-143
B:107-143
37
37
1.6eENST000003704736eENSE00000776340chr1:89524726-89524524203GBP1_HUMAN143-211692A:143-211 (gaps)
B:143-211 (gaps)
69
69
1.7ENST000003704737ENSE00001753781chr1:89523917-89523675243GBP1_HUMAN211-292822A:211-292
B:211-292
82
82
1.8aENST000003704738aENSE00001797851chr1:89522817-89522537281GBP1_HUMAN292-385942A:292-308
B:292-309
17
18
1.9aENST000003704739aENSE00001650939chr1:89521911-89521699213GBP1_HUMAN386-456710--
1.10cENST0000037047310cENSE00001675983chr1:89520898-89520796103GBP1_HUMAN457-491350--
1.10eENST0000037047310eENSE00001654998chr1:89520558-89520365194GBP1_HUMAN491-555650--
1.11dENST0000037047311dENSE00001883245chr1:89519151-895180021150GBP1_HUMAN556-592370--

(-) 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:288
 aligned with GBP1_HUMAN | P32455 from UniProtKB/Swiss-Prot  Length:592

    Alignment length:303
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305   
           GBP1_HUMAN     6 HMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDENENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGD 308
               SCOP domains d2b8wa1 A:6-283 automated matches                                                                                                                                                                                                                                                     d2b8wa2 A:284-308         SCOP domains
               CATH domains 2b8wA00 A:6-308 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..eeeehhhhhhhhhhh...eeeeeeee....hhhhhhhhhh..................eeeeeee.......eeeeeee.........hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhh.---------------.....eeeeeee......ee..ee.hhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------V-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------G_GB1_RHD3  PDB: A:35-278 UniProt: 35-278                                                                                                                                                                                                           ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:6-64 UniProt: 1-64 [INCOMPLETE]          ------------------------------------------Exon 1.6b  PDB: A:107-143            -------------------------------------------------------------------Exon 1.7  PDB: A:211-292 UniProt: 211-292                                         ---------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.5a  PDB: A:64-106 UniProt: 64-106   ------------------------------------Exon 1.6e  PDB: A:143-211 (gaps) UniProt: 143-211                    --------------------------------------------------------------------------------Exon 1.8a         Transcript 1 (2)
                 2b8w A   6 HMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKS---------------VSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGD 308
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155|        -      |175       185       195       205       215       225       235       245       255       265       275       285       295       305   
                                                                                                                                                                                156             172                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:290
 aligned with GBP1_HUMAN | P32455 from UniProtKB/Swiss-Prot  Length:592

    Alignment length:304
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305    
           GBP1_HUMAN     6 HMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDENENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDL 309
               SCOP domains d2b8wb1 B:6-283 automated matches                                                                                                                                                                                                                                                     d2b8wb2 B:284-309          SCOP domains
               CATH domains 2b8wB00 B:6-309 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..eeeehhhhhhhhh.....eeeeeeee....hhhhhhhhhhh.................eeeeeee.......eeeeeee.........hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhh.--------------.....eeeeeee......ee..ee.hhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------G_GB1_RHD3  PDB: B:35-278 UniProt: 35-278                                                                                                                                                                                                           ------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:6-64 UniProt: 1-64 [INCOMPLETE]          ------------------------------------------Exon 1.6b  PDB: B:107-143            -------------------------------------------------------------------Exon 1.7  PDB: B:211-292 UniProt: 211-292                                         ----------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.5a  PDB: B:64-106 UniProt: 64-106   ------------------------------------Exon 1.6e  PDB: B:143-211 (gaps) UniProt: 143-211                    --------------------------------------------------------------------------------Exon 1.8a          Transcript 1 (2)
                 2b8w B   6 HMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSS--------------VSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDL 309
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155 |       -      |175       185       195       205       215       225       235       245       255       265       275       285       295       305    
                                                                                                                                                                                 157            172                                                                                                                                         

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B8W)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GBP1_HUMAN | P32455)
molecular function
    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:0051879    Hsp90 protein binding    Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0019955    cytokine binding    Interacting selectively and non-covalently with a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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.
    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:0030507    spectrin binding    Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers.
biological process
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus 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:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0050860    negative regulation of T cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:1900041    negative regulation of interleukin-2 secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-2 secretion.
    GO:1903077    negative regulation of protein localization to plasma membrane    Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane.
    GO:1900025    negative regulation of substrate adhesion-dependent cell spreading    Any process that stops, prevents or reduces the frequency, rate or extent of substrate adhesion-dependent cell spreading.
    GO:0050848    regulation of calcium-mediated signaling    Any process that modulates the frequency, rate or extent of calcium-mediated signaling, the process in which a cell uses calcium ions to convert an extracellular signal into a response.
    GO:1903076    regulation of protein localization to plasma membrane    Any process that modulates the frequency, rate or extent of protein localization to plasma 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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GBP1_HUMAN | P324551dg3 1f5n 2b92 2bc9 2d4h

(-) Related Entries Specified in the PDB File

1dg3 THE FULL LENGTH PROTEIN WITH THE MUTATION H507Q AND IN ITS NUCLEOTIDE FREE FORM
1f5n THE FULL LENGTH PROTEIN WITH THE MUTATION H507Q AND IN COMPLEX WITH THE NON-HYDROLYZABLE GTP ANALOGUE GMPPNHP
2b92 THE SAME PROTEIN (HGBP1 N-TERMINAL LARGE GTPASE DOMAIN) IN COMPLEX WITH GDP/ALF3
2bc9 THE SAME PROTEIN (HGBP1 N-TERMINAL LARGE GTPASE DOMAIN) IN COMPLEX WITH THE NON-HYDROLYZABLE GTP ANALOGUE GMPPNHP
2d4h THE SAME PROTEIN (HGBP1 N-TERMINAL LARGE GTPASE DOMAIN) IN COMPLEX WITH GMP