1TPZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

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 :   16 Jun 04 (Deposition) - 21 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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)

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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:83 , GDP A:1500 , HOH A:1709 , HOH A:1710 , HOH A:1711 , HOH A:1712	BINDING SITE FOR RESIDUE MG A 1501
2	AC2	SOFTWARE	SER B:83 , GDP B:2500 , HOH B:2592 , HOH B:2635 , HOH B:2666 , HOH B:2693	BINDING SITE FOR RESIDUE MG B 2501
3	AC3	SOFTWARE	GLU A:77 , GLY A:79 , SER A:80 , GLY A:81 , LYS A:82 , SER A:83 , SER A:84 , THR A:102 , GLY A:103 , LYS A:184 , ASP A:186 , SER A:187 , SER A:231 , ASN A:232 , LYS A:233 , MG A:1501 , HOH A:1634 , HOH A:1636 , HOH A:1641 , HOH A:1690 , HOH A:1699 , HOH A:1709 , HOH A:1711 , HOH A:1712	BINDING SITE FOR RESIDUE GDP A 1500
4	AC4	SOFTWARE	GLY B:79 , SER B:80 , GLY B:81 , LYS B:82 , SER B:83 , SER B:84 , THR B:102 , GLY B:103 , LYS B:184 , ASP B:186 , SER B:231 , ASN B:232 , LYS B:233 , MG B:2501 , HOH B:2528 , HOH B:2592 , HOH B:2635 , HOH B:2660 , HOH B:2666	BINDING SITE FOR RESIDUE GDP B 2500
5	AC5	SOFTWARE	HIS B:116 , ASN B:118 , VAL B:261 , SER B:262 , LEU B:263 , LYS B:274 , VAL B:319 , HOH B:2705 , HOH B:2728	BINDING SITE FOR RESIDUE EDO B 2000
6	AC6	SOFTWARE	ASN B:265 , PHE B:320 , GLY B:321 , LEU B:330 , ALA B:402 , ILE B:409 , HOH B:2621	BINDING SITE FOR RESIDUE MPD B 1000

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_IRG	PS51716	IRG-type guanine nucleotide-binding (G) domain profile.	IIGP1_MOUSE	68-250	2	A:68-250 B:68-250

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_IRG	PS51716	IRG-type guanine nucleotide-binding (G) domain profile.	IIGP1_MOUSE	68-250	1	A:68-250 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_IRG	PS51716	IRG-type guanine nucleotide-binding (G) domain profile.	IIGP1_MOUSE	68-250	1	- B:68-250

(no "Exon" information available for 1TPZ)

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:395
 aligned with IIGP1_MOUSE | Q9QZ85 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:402
                                                                                                                                                                                                                                                                                                                                                                                                                                         413  
                                    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--   -
               SCOP domains d1tpza_ A: Interferon-inducible GTPase                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhh.....................eeee......eeeee..hhhhh..hhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhh...eeeeee.hhhhhhhhh..-------..hhhhhhhhhhhhhhhhh......eee.........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------G_IRG  PDB: A:68-250 UniProt: 68-250                                                                                                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tpz A  14 NDLPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISMMKKEFYFVRTKVDSDITNEAD-------KEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVSLPNITDSVIEKKRQFLKQRIWLEGFAADLVNIIPSLTFLLDSDLETLKKSMKFYRTVFGVDETSLQRLARDWEIEVDQVEAMIKSPAVFKPTDEETIQERLSRYIQEFCLANGYLLPKNSFLKEIFYLKYYFLDMVTEDAKTLLKEICLKLGR 415
                                    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  
                                                                                                                                                                                                              194     202

Chain B from PDB  Type:PROTEIN  Length:392
 aligned with IIGP1_MOUSE | Q9QZ85 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:402
                                                                                                                                                                                                                                                                                                                                                                                                                                         413  
                                    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--   -
               SCOP domains d1tpzb_ B: Interferon-inducible GTPase                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------------IIGP-1tpzB01 B:35-409                                                                                                                                                                                                                                                                                                                                                                  ------ Pfam domains (1)
           Pfam domains (2) ---------------------IIGP-1tpzB02 B:35-409                                                                                                                                                                                                                                                                                                                                                                  ------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhh.....................eeee......eeeee..hhhhhh.hhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhh----------..hhhhhhhhhhhhhhh.......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
                 1tpz B  14 NDLPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISMMKKEFYFVRTKVDSDITNE----------EKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVSLPNITDSVIEKKRQFLKQRIWLEGFAADLVNIIPSLTFLLDSDLETLKKSMKFYRTVFGVDETSLQRLARDWEIEVDQVEAMIKSPAVFKPTDEETIQERLSRYIQEFCLANGYLLPKNSFLKEIFYLKYYFLDMVTEDAKTLLKEICLKLGR 415
                                    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  
                                                                                                                                                                                                            192        203

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	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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: G proteins (693)

Protein domain: Interferon-inducible GTPase (5)

Mouse (Mus musculus) [TaxId: 10090] (5)

1a	d1tpza_	A:
1b	d1tpzb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: IIGP (4)

Mus musculus (Mouse) (4)

1a	IIGP-1tpzB01	B:35-409
1b	IIGP-1tpzB02	B:35-409

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tpz)

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

1dg3
1f5n
1tq2	THE SAME PROTEIN WITH GNP
1tq4	THE SAME PROTEIN, K48A MUTANT WITH GDP
1tq6	THE SAME PROTEIN, M173A MUTANT WITH GNP
1tqd	THE SAME PROTEIN WITHOUT NUCLEOTIDE

Description

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Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

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