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Title :   CRYSTAL STRUCTURE OF MNME FROM CHLOROBIUM TEPIDUM IN COMPLEX WITH GCP

Authors :   S. Meyer, A. Wittinghofer

Date :   25 Feb 09 (Deposition) - 27 Oct 09 (Release) - 27 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.40

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (2x)
Biol. Unit 2: B,C  (1x)

Keywords :   G Protein, G Domain, Gtpase, Gida, Trna Modification, U34, Gtp-Binding, Thf-Binding, Cytoplasm, Hydrolase, Magnesium, Metal-Binding, Nucleotide-Binding, Potassium, Trna Processing' (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Meyer, S. Bohme, A. Kruger, H. -J. Steinhoff, J. P. Klare, A. Wittinghofer
Kissing G Domains Of Mnme Monitored By X-Ray Crystallography And Pulse Electron Paramagnetic Resonance Spectroscopy
Plos Biol. V. 7 E1000 2009
PubMed-ID: 19806182 | Reference-DOI: 10.1371/JOURNAL.PBIO.1000212
(for further references see the PDB file header)

Molecule 1 - TRNA MODIFICATION GTPASE MNME
	Chains	:	A, B, C
	EC Number	:	3.6.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B-CTMNME
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MNME, CT2084, THDF, TRME
	Organism Scientific	:	CHLOROBIUM TEPIDUM
	Organism Taxid	:	1097
	Synonym	:	MNME

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GCP	2	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	GCP	2	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GCP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:238 , PRO A:239 , ASN A:240 , ALA A:241 , GLY A:242 , LYS A:243 , SER A:244 , THR A:245 , ASN A:348 , LYS A:349 , ASP A:351 , SER A:375 , ALA A:376 , LEU A:377 , MG A:475	BINDING SITE FOR RESIDUE GCP A 474
2	AC2	SOFTWARE	SER A:244 , GCP A:474	BINDING SITE FOR RESIDUE MG A 475
3	AC3	SOFTWARE	ASN B:240 , ALA B:241 , GLY B:242 , LYS B:243 , SER B:244 , THR B:245 , ASN B:348 , LYS B:349 , ASP B:351 , SER B:375 , ALA B:376 , LEU B:377	BINDING SITE FOR RESIDUE GCP B 474

(no "SS Bond" information available for 3GEI)

(no "Cis Peptide Bond" information available for 3GEI)

(no "SAP(SNP)/Variant" information available for 3GEI)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TRME	PS51709	TrmE-type guanine nucleotide-binding (G) domain profile.	MNME_CHLTE	230-394	3	A:230-394 B:230-394 C:230-230

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TRME	PS51709	TrmE-type guanine nucleotide-binding (G) domain profile.	MNME_CHLTE	230-394	2	A:230-394 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TRME	PS51709	TrmE-type guanine nucleotide-binding (G) domain profile.	MNME_CHLTE	230-394	2	- B:230-394 C:230-230

(no "Exon" information available for 3GEI)

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:428
 aligned with MNME_CHLTE | Q8KAS1 from UniProtKB/Swiss-Prot  Length:473

    Alignment length:470
                                    13        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       423       433       443       453       463       473
           MNME_CHLTE     4 SDLHLPVPGHPIAAIATPVGVGALAIVRISGAGVLDLADRVFRKVHGSGKLAEAAGYTAHFGRLYDGEEMVDEVIALVFRAPRSFTAEQMVEFTCHGGPVVVGRVLRLMLDNGCRLAEPGEFTRRAFLNGRIDLLQAEAIGEMIHARTESAYRTAVSQMKGDLSVRLGGLREQLIRSCALIELELDFSEEDVEFQSRDELTMQIETLRSEVNRLIDSYQHGRIVSEGVSTVIAGKPNAGKSTLLNTLLGQERAIVSHMPGTTRDYIEECFIHDKTMFRLTDTAGLREAGEEIEHEGIRRSRMKMAEADLILYLLDLGTERLDDELTEIRELKAAHPAAKFLTVANKLDRAANADALIRAIADGTGTEVIGISALNGDGIDTLKQHMGDLVKNLDKLHEASVLVTSLRHYEALRNASDALQNALELIAHESETELIAFELRAALDYVGQITGKVVNEEVLNTIFDKFCIGK 473
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3geiA01 A:4-134 Probable tRNA modification gtpase trme; domain 1                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee........eeeeeee..hhhhhhhh.eee.............eeeeeeeee..eeeeeeeeeee..........eeeeeee.hhhhhhhhhhhhhhh..ee...hhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee.....hhhhhhhhhh------------------..eeee..eeeeee.--------------------.......eeeeeee.........hhhhhhhhhhh...eeeeeee.......hhhhhhhhhhh....eee.......hhhhhhhhhh......----.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G_TRME  PDB: A:230-394 UniProt: 230-394                                                                                                                              ------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gei A   4 SDLHLPVPGHPIAAIATPVGVGALAIVRISGAGVLDLADRVFRKVHGSGKLAEAAGYTAHFGRLYDGEEMVDEVIALVFRAPRSFTAEQMVEFTCHGGPVVVGRVLRLMLDNGCRLAEPGEFTRRAFLNGRIDLLQAEAIGEMIHARTESAYRTAVSQMKGDLSVRLGGLREQLIRSCALIELELDFSEEDVEFQSRDELTMQIETLRSEVNRLIDSYQHGRIVSEGVSTVIAGKPNAGKSTLLNTLL------------------EECFIHDKTMFRLTD--------------------MKMAEADLILYLLDLGTERLDDELTEIRELKAAHPAAKFLTVANKLDRAANADALIRAIADGTGTEVIGISALNGDGIDTLKQHMGDLVKNL----EASVLVTSLRHYEALRNASDALQNALELIAHESETELIAFELRAALDYVGQITGKVVNEEVLNTIFDKFCIGK 473
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       | -         -      |273       283|        -         - |     313       323       333       343       353       363       373       383       393  |    403       413       423       433       443       453       463       473
                                                                                                                                                                                                                                                                                 251                270           284                  305                                                                                        396  401

Chain B from PDB  Type:PROTEIN  Length:424
 aligned with MNME_CHLTE | Q8KAS1 from UniProtKB/Swiss-Prot  Length:473

    Alignment length:470
                                    13        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       423       433       443       453       463       473
           MNME_CHLTE     4 SDLHLPVPGHPIAAIATPVGVGALAIVRISGAGVLDLADRVFRKVHGSGKLAEAAGYTAHFGRLYDGEEMVDEVIALVFRAPRSFTAEQMVEFTCHGGPVVVGRVLRLMLDNGCRLAEPGEFTRRAFLNGRIDLLQAEAIGEMIHARTESAYRTAVSQMKGDLSVRLGGLREQLIRSCALIELELDFSEEDVEFQSRDELTMQIETLRSEVNRLIDSYQHGRIVSEGVSTVIAGKPNAGKSTLLNTLLGQERAIVSHMPGTTRDYIEECFIHDKTMFRLTDTAGLREAGEEIEHEGIRRSRMKMAEADLILYLLDLGTERLDDELTEIRELKAAHPAAKFLTVANKLDRAANADALIRAIADGTGTEVIGISALNGDGIDTLKQHMGDLVKNLDKLHEASVLVTSLRHYEALRNASDALQNALELIAHESETELIAFELRAALDYVGQITGKVVNEEVLNTIFDKFCIGK 473
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3geiB01 B:4-134 Probable tRNA modification gtpase trme; domain 1                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee........eeeeeee..hhhhhhhh.eee.............eeeeeeeee..eeeeeeeeeee..........eeeeeee.hhhhhhhhhhhhhhh..ee...hhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee.....hhhhhhhhhh------------------..eeee..eeeeee.--------------------.......eeeeeee.........hhhhhhhhhhh...eeeeeee.......hhhhhhhhhhh....eee.......hhhhhhhhhh....--------.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G_TRME  PDB: B:230-394 UniProt: 230-394                                                                                                                              ------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gei B   4 SDLHLPVPGHPIAAIATPVGVGALAIVRISGAGVLDLADRVFRKVHGSGKLAEAAGYTAHFGRLYDGEEMVDEVIALVFRAPRSFTAEQMVEFTCHGGPVVVGRVLRLMLDNGCRLAEPGEFTRRAFLNGRIDLLQAEAIGEMIHARTESAYRTAVSQMKGDLSVRLGGLREQLIRSCALIELELDFSEEDVEFQSRDELTMQIETLRSEVNRLIDSYQHGRIVSEGVSTVIAGKPNAGKSTLLNTLL------------------EECFIHDKTMFRLTD--------------------MKMAEADLILYLLDLGTERLDDELTEIRELKAAHPAAKFLTVANKLDRAANADALIRAIADGTGTEVIGISALNGDGIDTLKQHMGDLVK--------SVLVTSLRHYEALRNASDALQNALELIAHESETELIAFELRAALDYVGQITGKVVNEEVLNTIFDKFCIGK 473
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       | -         -      |273       283|        -         - |     313       323       333       343       353       363       373       383       393|      403       413       423       433       443       453       463       473
                                                                                                                                                                                                                                                                                 251                270           284                  305                                                                                      394      403

Chain C from PDB  Type:PROTEIN  Length:298
 aligned with MNME_CHLTE | Q8KAS1 from UniProtKB/Swiss-Prot  Length:473

    Alignment length:470
                                    13        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       423       433       443       453       463       473
           MNME_CHLTE     4 SDLHLPVPGHPIAAIATPVGVGALAIVRISGAGVLDLADRVFRKVHGSGKLAEAAGYTAHFGRLYDGEEMVDEVIALVFRAPRSFTAEQMVEFTCHGGPVVVGRVLRLMLDNGCRLAEPGEFTRRAFLNGRIDLLQAEAIGEMIHARTESAYRTAVSQMKGDLSVRLGGLREQLIRSCALIELELDFSEEDVEFQSRDELTMQIETLRSEVNRLIDSYQHGRIVSEGVSTVIAGKPNAGKSTLLNTLLGQERAIVSHMPGTTRDYIEECFIHDKTMFRLTDTAGLREAGEEIEHEGIRRSRMKMAEADLILYLLDLGTERLDDELTEIRELKAAHPAAKFLTVANKLDRAANADALIRAIADGTGTEVIGISALNGDGIDTLKQHMGDLVKNLDKLHEASVLVTSLRHYEALRNASDALQNALELIAHESETELIAFELRAALDYVGQITGKVVNEEVLNTIFDKFCIGK 473
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3geiC01 C:4-134 Probable tRNA modification gtpase trme; domain 1                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee........eeeeeee..hhhhhhhh.eee.............eeeeeeeee..eeeeeeeeeee..........eeeeeee.hhhhhhhhhhhhhhh..ee...hhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G_TRME  PDB: C:230-230 UniProt: 230-394                                                                                                                              ------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gei C   4 SDLHLPVPGHPIAAIATPVGVGALAIVRISGAGVLDLADRVFRKVHGSGKLAEAAGYTAHFGRLYDGEEMVDEVIALVFRAPRSFTAEQMVEFTCHGGPVVVGRVLRLMLDNGCRLAEPGEFTRRAFLNGRIDLLQAEAIGEMIHARTESAYRTAVSQMKGDLSVRLGGLREQLIRSCALIELELDFSEEDVEFQSRDELTMQIETLRSEVNRLIDSYQHGRIVSEG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------SVLVTSLRHYEALRNASDALQNALELIAHESETELIAFELRAALDYVGQITGKVVNEEVLNTIFDKFCIGK 473
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223      |  -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       403       413       423       433       443       453       463       473
                                                                                                                                                                                                                                                            230                                                                                                                                                                          403

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 '\|'

(no "SCOP Domain" information available for 3GEI)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Gyrase A; domain 2 (166)

Homologous Superfamily: Probable tRNA modification gtpase trme; domain 1 (18)

Chlorobium tepidum. Organism_taxid: 1097. (2)

1a	3geiA01	A:4-134
1b	3geiB01	B:4-134
1c	3geiC01	C:4-134

(no "Pfam Domain" information available for 3GEI)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (MNME_CHLTE | Q8KAS1)

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: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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0006400	tRNA modification	The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric Unit
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	MNME_CHLTE \| Q8KAS1	:	3gee

1rfl	NMR DATA DRIVEN STRUCTURAL MODEL OF G-DOMAIN OF MNME PROTEIN
1xzp	GTP-BINDING PROTEIN TRME
1xzq	STRUCTURE OF THE GTP-BINDING PROTEIN TRME FROM THERMOTOGA MARITIMA COMPLEXED WITH 5-FORMYL-THF
2gj8	MNME G-DOMAIN IN COMPLEX WITH GDP-ALF4-, MG2+ AND K+
2gj9	MNME G-DOMAIN IN COMPLEX WITH GDP-ALF4-, MG2+ AND RB+
2gja	STRUCTURE OF THE MNME G-DOMAIN IN COMPLEX WITH GDP*ALF4-, MG2+ AND NH4+
3cp2	GIDA FROM ESCHERICHIA COLI
3cp8	GIDA FROM CHLOROBIUM TEPIDUM
3gee	MNME FROM CHLOROBIUM TEPIDUM IN COMPLEX WITH FOLINIC ACID AND GDP
3geh	MNME FROM NOSTOC AZOLLAE IN COMPLEX WITH FOLINIC ACID GDP AND ZN

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