Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
46  structures 725  species 0  interactions 5313  sequences 133  architectures

Family: GBP (PF02263)

Summary: Guanylate-binding protein, N-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Guanylate-binding protein". More...

Guanylate-binding protein Edit Wikipedia article

Guanylate-binding protein, N-terminal domain
PDB 1dg3 EBI.jpg
structure of human guanylate binding protein-1 in nucleotide free form
Identifiers
SymbolGBP
PfamPF02263
Pfam clanCL0023
InterProIPR015894
SCOPe1dg3 / SUPFAM
Guanylate-binding protein, C-terminal domain
PDB 1dg3 EBI.jpg
structure of human guanylate binding protein-1 in nucleotide free form
Identifiers
SymbolGBP_C
PfamPF02841
InterProIPR003191
SCOPe1dg3 / SUPFAM

In molecular biology, the guanylate-binding protein family is a family of GTPases that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma (Interferon-inducible GTPase) are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-KD immunity-related GTPases (IRGs), the Mx proteins (MX1, MX2), and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class. In humans, there are seven GBPs (hGBP1-7).[1] Structurally, hGBP1 consists of two domains: a compact globular N-terminal domain harbouring the GTPase function, and an alpha-helical finger-like C-terminal domain.[2] Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma.[3]

References

  1. ^ Tripal P, Bauer M, Naschberger E, Mortinger T, Hohenadl C, Cornali E, Thurau M, Sturzl M (January 2007). "Unique features of different members of the human guanylate-binding protein family". J. Interferon Cytokine Res. 27 (1): 44–52. doi:10.1089/jir.2007.0086. PMID 17266443.
  2. ^ Prakash B, Praefcke GJ, Renault L, Wittinghofer A, Herrmann C. Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins. Nature. 2000 Feb 3;403(6769):567-71. http://www.nature.com/nature/journal/v403/n6769/full/403567a0.html
  3. ^ Naschberger E, Lubeseder-Martellato C, Meyer N, Gessner R, Kremmer E, Gessner A, Sturzl M (September 2006). "Human guanylate binding protein-1 is a secreted GTPase present in increased concentrations in the cerebrospinal fluid of patients with bacterial meningitis". Am. J. Pathol. 169 (3): 1088–99. doi:10.2353/ajpath.2006.060244. PMC 1698817. PMID 16936281.
This article incorporates text from the public domain Pfam and InterPro: IPR003191
This article incorporates text from the public domain Pfam and InterPro: IPR015894

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Guanylate-binding protein, N-terminal domain Provide feedback

Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.

Literature references

  1. Prakash B, Praefcke GJ, Renault L, Wittinghofer A, Herrmann C; , Nature 2000;403:567-571.: Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins. PUBMED:10676968 EPMC:10676968


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015894

Guanylate-binding protein is a GTPase that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-kd GTPases, the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class. In humans, there are seven GBPs (hGBP1-7) [ PUBMED:17266443 ]. Structurally, hGBP1 consists of two domains: a compact globular N-terminal domain harbouring the GTPase function, and an alpha-helical finger-like C-terminal domain ( INTERPRO ). Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma [ PUBMED:16936281 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 243 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp bpMoxR Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DBINO DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF5906 DUF6079 DUF815 DUF853 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK HSA HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1C Lon_2 LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB Mur_ligase_M MutS_V Myosin_head NACHT NAT_N NB-ARC NOG1 NTPase_1 NTPase_P4 OPA1_C ORC3_N P-loop_TraG ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3 RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom Spore_III_AA Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6N Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YqeC Zeta_toxin Zot

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(12)
Full
(5313)
Representative proteomes UniProt
(10151)
RP15
(1037)
RP35
(2392)
RP55
(4567)
RP75
(5811)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(12)
Full
(5313)
Representative proteomes UniProt
(10151)
RP15
(1037)
RP35
(2392)
RP55
(4567)
RP75
(5811)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(12)
Full
(5313)
Representative proteomes UniProt
(10151)
RP15
(1037)
RP35
(2392)
RP55
(4567)
RP75
(5811)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_4308 (release 5.2) & Pfam-B_9065 (release 8.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Mian N , Griffiths-Jones SR
Number in seed: 12
Number in full: 5313
Average length of the domain: 221.10 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 38.27 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 260
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the GBP domain has been found. There are 46 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JDV3 View 3D Structure Click here
A0A0P0WQZ8 View 3D Structure Click here
A0A0R0L6C9 View 3D Structure Click here
A0A0R4IPT3 View 3D Structure Click here
A0A0R4IQI6 View 3D Structure Click here
A0A0R4ITT0 View 3D Structure Click here
A0A1D6H3C9 View 3D Structure Click here
A0A1D6H4M6 View 3D Structure Click here
A0A1D6HFN9 View 3D Structure Click here
A0A1D6HTN6 View 3D Structure Click here
A0A1D6L7P3 View 3D Structure Click here
A0A1D6MCT0 View 3D Structure Click here
A0A1D6Q5W7 View 3D Structure Click here
A0A2R8Q6Y1 View 3D Structure Click here
A0A2R8QDK8 View 3D Structure Click here
A0A2R8QIF8 View 3D Structure Click here
A0A2R8RX84 View 3D Structure Click here
A4UUI3 View 3D Structure Click here
A9YVJ5 View 3D Structure Click here
B0V1H4 View 3D Structure Click here
B8A2V3 View 3D Structure Click here
D3ZJ56 View 3D Structure Click here
D3ZKU6 View 3D Structure Click here
D3ZQL3 View 3D Structure Click here
D3ZV82 View 3D Structure Click here
E7F219 View 3D Structure Click here
E9QF26 View 3D Structure Click here
E9QGX9 View 3D Structure Click here
F1LQ09 View 3D Structure Click here
F1LVN3 View 3D Structure Click here
F1M9F6 View 3D Structure Click here
F1QUY8 View 3D Structure Click here
F4I2I5 View 3D Structure Click here
F4ITY5 View 3D Structure Click here
F4KG14 View 3D Structure Click here
F6NJS4 View 3D Structure Click here
I1KLQ4 View 3D Structure Click here
I1L889 View 3D Structure Click here
I1M057 View 3D Structure Click here
I1M1Y5 View 3D Structure Click here
K7V1D8 View 3D Structure Click here
M0RDF8 View 3D Structure Click here
O62433 View 3D Structure Click here
O70418 View 3D Structure Click here
P32455 View 3D Structure Click here
P32456 View 3D Structure Click here
Q000W5 View 3D Structure Click here
Q01514 View 3D Structure Click here
Q0D863 View 3D Structure Click here
Q0ZHH6 View 3D Structure Click here
Q1MT80 View 3D Structure Click here
Q54PI3 View 3D Structure Click here
Q54TN9 View 3D Structure Click here
Q61107 View 3D Structure Click here
Q63663 View 3D Structure Click here
Q6DD88 View 3D Structure Click here
Q6DHP7 View 3D Structure Click here
Q6K2Y3 View 3D Structure Click here
Q6PA06 View 3D Structure Click here
Q6PST4 View 3D Structure Click here
Q6ZN66 View 3D Structure Click here
Q8BH66 View 3D Structure Click here
Q8BTS3 View 3D Structure Click here
Q8CFB4 View 3D Structure Click here
Q8IKL1 View 3D Structure Click here
Q8IKL1 View 3D Structure Click here
Q8N8V2 View 3D Structure Click here
Q8NHH9 View 3D Structure Click here
Q8WXF7 View 3D Structure Click here
Q91YH5 View 3D Structure Click here
Q91Z40 View 3D Structure Click here
Q96DY5 View 3D Structure Click here
Q96PP8 View 3D Structure Click here
Q96PP9 View 3D Structure Click here
Q9BMU4 View 3D Structure Click here
Q9H0R5 View 3D Structure Click here
Q9ULX5 View 3D Structure Click here
Q9VC57 View 3D Structure Click here
Q9Z0E6 View 3D Structure Click here