3NAG - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) SYNTHETASE FROM THERMOPLASMA VOLCANIUM IN COMPLEX WITH ADP

Authors :   M. M. Cherney, L. T. Cherney, C. R. Garen, M. N. G. James

Date :   02 Jun 10 (Deposition) - 08 Jun 11 (Release) - 25 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Phosphoribosyl Transferase, Adp Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. M. Cherney, L. T. Cherney, C. R. Garen, M. N. James
The Structures Of Thermoplasma Volcanium Phosphoribosyl Pyrophosphate Synthetase Bound To Ribose-5-Phosphate And At Analogs.
J. Mol. Biol. V. 413 844 2011
PubMed-ID: 21963988 | Reference-DOI: 10.1016/J.JMB.2011.09.007

Molecule 1 - RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
	Chains	:	A, B
	EC Number	:	2.7.6.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP16
	Expression System Strain	:	BL21 (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PRS, TV0197, TVG0201915, TVN0197
	Organism Scientific	:	THERMOPLASMA VOLCANIUM GSS1
	Organism Taxid	:	273116
	Strain	:	ATCC51530
	Synonym	:	RPPK, PHOSPHORIBOSYL PYROPHOSPHATE SYNTHASE, P-RIB-PP SYNTHASE, PRPP SYNTHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 14)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:214 , THR A:215 , GLY A:216 , GLY A:217 , THR A:218 , HOH A:395 , HOH A:436	BINDING SITE FOR RESIDUE SO4 A 287
2	AC2	SOFTWARE	ARG A:7 , SER A:58 , ALA A:60 , HOH A:294 , HOH A:336 , HOH A:379	BINDING SITE FOR RESIDUE SO4 A 288
3	AC3	SOFTWARE	LYS A:11 , ARG A:15	BINDING SITE FOR RESIDUE SO4 A 289
4	AC4	SOFTWARE	PHE A:32 , ASP A:34 , GLU A:36 , HOH A:295 , ARG B:40 , ARG B:91 , GLN B:92 , HIS B:93 , TYR B:96 , MG B:287 , HOH B:388 , HOH B:389 , HOH B:400 , HOH B:414 , HOH B:522	BINDING SITE FOR RESIDUE ADP B 300
5	AC5	SOFTWARE	HIS B:124 , ADP B:300 , HOH B:355 , HOH B:389	BINDING SITE FOR RESIDUE MG B 287
6	AC6	SOFTWARE	ARG B:91 , ILE B:213 , SER B:214 , THR B:215 , GLY B:216 , GLY B:217 , THR B:218 , HOH B:332 , HOH B:468 , HOH B:474 , HOH B:510	BINDING SITE FOR RESIDUE SO4 B 288
7	AC7	SOFTWARE	ARG B:7 , SER B:58 , HOH B:352 , HOH B:530	BINDING SITE FOR RESIDUE SO4 B 289
8	AC8	SOFTWARE	LYS B:195 , ASN B:198 , LYS B:229 , HOH B:344 , HOH B:505	BINDING SITE FOR RESIDUE SO4 B 290

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

Asymmetric Unit

No.	Residues
1	Gln A:92	-	His A:93
2	Tyr A:96	-	Lys A:97
3	Val A:196	-	Pro A:197
4	Asn A:245	-	Gly A:246
5	Val B:196	-	Pro B:197

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

(no "PROSITE Motif" information available for 3NAG)

(no "Exon" information available for 3NAG)

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:284
 aligned with KPRS_THEVO | Q97CA5 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           KPRS_THEVO     1 MKIIALRSSLKLAARIAEELKTEPVMPDERRFPDGELYLRYDEDLTGHNIFIIGNTHSDAEVMEMILTLSAIQDYRTKSVNIIAPYYGYARQHQRYKNGEPISSQILTEIYSSYSNSIATVDIHDEKTLSYSKVKFSDLHANDAIVRYYKNVDVDYVVSPDDGGLARVADISAKLGKKHFFIEKKRIDDRTVEMKVPNVDVNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENKILQNADEIHVTDTVESKFSDISVYQEVCNYIRDI 284
               SCOP domains d3naga1 A:1-155 automated matches                                                                                                                          d3naga2 A:156-284 automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee..eeee.....eeee........eeeee....hhhhhhhhhhhhhhhhhh...eeeeee.................hhhhhhhhhhhhh..eeeee...hhhhhhhh...eeee.hhhhhhhhhh.....eeee....hhhhhhhhhhhhh.eeeeeeeeee..eeeeeee........eeeeeeeee..hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhh....eeeee.......eee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nag A   1 MKIIALRSSLKLAARIAEELKTEPVMPDERRFPDGELYLRYDEDLTGHNIFIIGNTHSDAEVMEMILTLSAIQDYRTKSVNIIAPYYGYARQHQRYKNGEPISSQILTEIYSSYSNSIATVDIHDEKTLSYSKVKFSDLHANDAIVRYYKNVDVDYVVSPDDGGLARVADISAKLGKKHFFIEKKRIDDRTVEMKVPNVDVNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENKILQNADEIHVTDTVESKFSDISVYQEVCNYIRDI 284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with KPRS_THEVO | Q97CA5 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:286
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280      
           KPRS_THEVO     1 MKIIALRSSLKLAARIAEELKTEPVMPDERRFPDGELYLRYDEDLTGHNIFIIGNTHSDAEVMEMILTLSAIQDYRTKSVNIIAPYYGYARQHQRYKNGEPISSQILTEIYSSYSNSIATVDIHDEKTLSYSKVKFSDLHANDAIVRYYKNVDVDYVVSPDDGGLARVADISAKLGKKHFFIEKKRIDDRTVEMKVPNVDVNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENKILQNADEIHVTDTVESKFSDISVYQEVCNYIRDIDA 286
               SCOP domains d3nagb1 B:1-155 automated matches                                                                                                                          d3nagb2 B:156-286 automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Pribosyltran_N-3nagB03 B:1-114                                                                                    --------------------Pribosyltran-3nagB01 B:135-240                                                                            ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) Pribosyltran_N-3nagB04 B:1-114                                                                                    --------------------Pribosyltran-3nagB02 B:135-240                                                                            ---------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee..eeee.....eeee........eeeee....hhhhhhhhhhhhhhhhhh...eeeeee.................hhhhhhhhhhhhh..eeeee...hhhhhhhh..eeeee.hhhhhhhhhh.....eeee....hhhhhhhhhhhhh.eeeeeeeeee..eeeeeee........eeeeeeeee..hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhh...eeeee.......eee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nag B   1 MKIIALRSSLKLAARIAEELKTEPVMPDERRFPDGELYLRYDEDLTGHNIFIIGNTHSDAEVMEMILTLSAIQDYRTKSVNIIAPYYGYARQHQRYKNGEPISSQILTEIYSSYSNSIATVDIHDEKTLSYSKVKFSDLHANDAIVRYYKNVDVDYVVSPDDGGLARVADISAKLGKKHFFIEKKRIDDRTVEMKVPNVDVNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENKILQNADEIHVTDTVESKFSDISVYQEVCNYIRDIDA 286
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: PRTase-like (145)

Superfamily: PRTase-like (145)

Family: automated matches (39)

Protein domain: automated matches (39)

Thermoplasma volcanium [TaxId: 273116] (1)

1a	d3naga1	A:1-155
1b	d3naga2	A:156-284
1c	d3nagb1	B:1-155
1d	d3nagb2	B:156-286

(no "CATH Domain" information available for 3NAG)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KPRS_THEVO | Q97CA5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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.
	GO:0004749	ribose phosphate diphosphokinase activity	Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H(+).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006015	5-phosphoribose 1-diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.
	GO:0009116	nucleoside metabolic process	The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0009156	ribonucleoside monophosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
		Asn A:245 - Gly A:246	[ RasMol ]
		Gln A:92 - His A:93	[ RasMol ]
		Tyr A:96 - Lys A:97	[ RasMol ]
		Val A:196 - Pro A:197	[ RasMol ]
		Val B:196 - Pro B:197	[ RasMol ]

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	KPRS_THEVO \| Q97CA5	:	3lpn 3lrt 3mbi

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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