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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURAL ANALYSIS OF THE DOMAIN INTERACTIONS IN DER, A SWITCH PROTEIN CONTAINING TWO GTPASE DOMAINS

Authors :   V. L. Robinson, J. Hwang, E. Fox, M. Inouye, A. M. Stock

Date :   29 Aug 02 (Deposition) - 14 Jan 03 (Release) - 04 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Gtpase, Enga, Der, Kh-Domain, Tandem G-Domains, Ligand Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. L. Robinson, J. Hwang, E. Fox, M. Inouye, A. M. Stock
Domain Arrangement Of Der, A Switch Protein Containing Two Gtpase Domains
Structure V. 10 1649 2002
PubMed-ID: 12467572 | Reference-DOI: 10.1016/S0969-2126(02)00905-X
(for further references see the PDB file header)

Molecule 1 - PROBABLE GTP-BINDING PROTEIN ENGA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	834(PLYSS)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TWO GTPASE DOMAINS
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Other Details	:	PROBABLE GTPASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 13)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MSE	7	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	5	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:11 , VAL A:12 , GLY A:13 , LYS A:14 , SER A:15 , PO4 A:602 , HOH A:674 , HOH A:812	BINDING SITE FOR RESIDUE PO4 A 601
2	AC2	SOFTWARE	LYS A:14 , CYS A:57 , PO4 A:601 , HOH A:694	BINDING SITE FOR RESIDUE PO4 A 602
3	AC3	SOFTWARE	SER A:68 , GLN A:69 , LYS A:70 , GLU A:172 , GLN A:280 , HOH A:753	BINDING SITE FOR RESIDUE PO4 A 603
4	AC4	SOFTWARE	LYS A:72 , LYS A:108 , ARG A:279 , ARG A:283 , HOH A:795	BINDING SITE FOR RESIDUE PO4 A 604
5	AC5	SOFTWARE	GLU A:100 , LYS A:203 , GLU A:204	BINDING SITE FOR RESIDUE PO4 A 605
6	AC6	SOFTWARE	ASN A:190 , VAL A:191 , GLY A:192 , LYS A:193 , SER A:194 , THR A:195 , ASN A:300 , LYS A:301 , ASP A:303 , LEU A:304 , SER A:335 , ALA A:336 , ASP A:337 , HOH A:695 , HOH A:820 , HOH A:851	BINDING SITE FOR RESIDUE GDP A 500

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

Asymmetric/Biological Unit

No.	Residues
1	Lys A:393	-	Pro A:394

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_ENGA	PS51712	EngA-type guanine nucleotide-binding (G) domain profile.	DER_THEMA	2-168 181-357	2	A:2-168 A:181-357

(no "Exon" information available for 1MKY)

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
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Chain A from PDB  Type:PROTEIN  Length:407
 aligned with DER_THEMA | Q9X1F8 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:438
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431        
            DER_THEMA     2 ATVLIVGRPNVGKSTLFNKLVKKKKAIVEDEEGVTRDPVQDTVEWYGKTFKLVDTCGVFDNPQDIISQKMKEVTLNMIREADLVLFVVDGKRGITKEDESLADFLRKSTVDTILVANKAENLREFEREVKPELYSLGFGEPIPVSAEHNINLDTLLETIIKKLEEKGLDLESKPEITDAIKVAIVGRPNVGKSTLFNAILNKERALVSPIPGTTRDPVDDEVFIDGRKYVFVDTAGLRRKSRVEPRTVEKYSNYRVVDSIEKADVVVIVLDATQGITRQDQRIAGLVERRGRASVVVFNKWDLVEHREKRYDEFTKLFREKLYFIDYSPLIFTSADKGWNIDRVIDAINLAYASYTTKVPSSAINSALQKVLAFTNLPRGLKIFFGLQVDIKPPTFLFFVNSIEKVKNPQKIFLRKLIRDYVFPFEGSPIFLKFKRSR 439
               SCOP domains d1mkya1 A:2-172 Probab              le GTPase Der, N-terminal and middle domains                                                                                           d1mkya2 A:173-358 Probable GTPase Der, N      -terminal and middle            domains                                                                                                     d1mkya3 A:359-439 Probable GTPase Der, C-terminal domain                          SCOP domains
               CATH domains -1mkyA01 A:3-172 P-loo              p containing nucleotide triphosphate hydrolases                                                                                        ------1mkyA02 A:179-347 P-loop containin      g nucleotide triphos           phate hydrolases                                                                                  --1mkyA03 A:350-439  [code=3.30.300.20, no name defined]                                     CATH domains
           Pfam domains (1) ----------------------              ------------------------------------------------------------------------------------------------------------------------------------------------MMR_HSR1-1mkyA01 A:182-301                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------              ------------------------------------------------------------------------------------------------------------------------------------------------MMR_HSR1-1mkyA02 A:182-301                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeeee.....hhhhhhhhhhh--------------...eeeeee..eeeeeee......hhhhh.hhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh.............eeeeee.....hhhhhhhhhhh...eee....------..eeeee..eeeee......-----------....hhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhh.hhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........eeeeeeee....eeeeee......hhhhhhhhhhhhhhhh........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE G_ENGA  PDB: A:2-168 UniProt: 2-168                                                                                                                                    ------------G_ENGA  PDB: A:181-357 UniProt: 181-357                                                                                                                                          ---------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mky A   2 ATVLIVGRPNVGKSTLFNKLVK--------------DPVQDTVEWYGKTFKLVDTCGVFDNPQDIISQKmKEVTLNmIREADLVLFVVDGKRGITKEDESLADFLRKSTVDTILVANKAENLREFEREVKPELYSLGFGEPIPVSAEHNINLDTmLETIIKKLEEKGLDLESKPEITDAIKVAIVGRPNVGKSTLFNAILNKERALVSPIP------VDDEVFIDGRKYVFVDTAGL-----------EKYSNYRVVDSIEKADVVVIVLDATQGITRQDQRmAGLmERRGRASVVVFNKWDLVVHREKRYDEFTKLFREKLYFIDYSPLIFTSADKGWNIDRmIDAmNLAYASYTTKVPSSAINSALQKVLAFTNLPRGLKIFFGVQVDIKPPTFLFFVNSIEKVKNPQKIFLRKLIRDYVFPFEGSPIFLKFKRSR 439
                                    11        21 |       -      | 41        51        61        71      | 81        91       101       111       121       131       141       151    |  161       171       181       191       201       211|      221       231      |  -       251       261       271       281  |   |291       301       311       321       331       341   |   351       361       371       381       391       401       411       421       431        
                                                23             38                               71-MSE 78-MSE                                                                       156-MSE                                                 212    219                238         250                               284-MSE                                                      345-MSE                                                                                          
                                                                                                                                                                                                                                                                                                                        288-MSE                                                      349-MSE

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: GMP Synthetase; Chain A, domain 3 (192)

Homologous Superfamily: [code=3.30.300.20, no name defined] (129)

Thermotoga maritima. Organism_taxid: 2336. (2)

1mkyA03

A:350-439

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Thermotoga maritima. Organism_taxid: 2336. (3)

2a	1mkyA01	A:3-172
2b	1mkyA02	A:179-347

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: MMR_HSR1 (17)

Thermotoga maritima (5)

1a	MMR_HSR1-1mkyA01	A:182-301
1b	MMR_HSR1-1mkyA02	A:182-301

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DER_THEMA | Q9X1F8)

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:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Lys A:393 - Pro A:394	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (3, 13)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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