1DKU - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.

Authors :   T. A. Eriksen, A. Kadziola, A. -K. Bentsen, K. W. Harlow, S. Larsen

Date :   08 Dec 99 (Deposition) - 05 Apr 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (3x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Open Alpha-Beta Structure, Domain Duplication, Phosphoribosyltransferase Type I Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. A. Eriksen, A. Kadziola, A. K. Bentsen, K. W. Harlow, S. Larsen
Structural Basis For The Function Of Bacillus Subtilis Phosphoribosyl-Pyrophosphate Synthetase.
Nat. Struct. Biol. V. 7 303 2000
PubMed-ID: 10742175 | Reference-DOI: 10.1038/74069
(for further references see the PDB file header)

Molecule 1 - PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
	Chains	:	A, B
	EC Number	:	2.7.6.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAB600
	Expression System Strain	:	HO773, IV
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	RIBOSE-PHOSPHATE PYROPHOSPHOKINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ABM	2	Ligand/Ion	METHYL PHOSPHONIC ACID ADENOSINE ESTER
2	AP2	2	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ABM	2	Ligand/Ion	METHYL PHOSPHONIC ACID ADENOSINE ESTER
2	AP2	2	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	ABM	6	Ligand/Ion	METHYL PHOSPHONIC ACID ADENOSINE ESTER
2	AP2	6	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	ABM	1	Ligand/Ion	METHYL PHOSPHONIC ACID ADENOSINE ESTER
2	AP2	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:105 , SER A:108 , ARG A:109 , SER B:52 , ARG B:54 , GLN B:140 , ASP B:148 , HIS B:149 , SER B:310 , VAL B:311 , SER B:312 , PHE B:315 , HOH B:1005 , HOH B:1006 , HOH B:1029	BINDING SITE FOR RESIDUE AP2 B 1001
2	AC2	SOFTWARE	SER A:52 , ARG A:54 , GLN A:140 , ASP A:148 , HIS A:149 , SER A:310 , VAL A:311 , SER A:312 , PHE A:315 , HOH A:1010 , LYS B:105 , ALA B:106 , ARG B:107 , SER B:108 , ARG B:109 , HOH B:1045	BINDING SITE FOR RESIDUE AP2 A 1002
3	AC3	SOFTWARE	ARG A:101 , GLN A:102 , ALA A:106 , HIS A:135 , HOH A:1046 , HOH A:1096 , HOH A:1097 , HOH A:1098 , PHE B:40 , ASP B:42 , GLU B:44	BINDING SITE FOR RESIDUE ABM A 1003
4	AC4	SOFTWARE	PHE A:40 , ASP A:42 , GLU A:44 , ARG B:101 , GLN B:102 , ARG B:104 , ALA B:106 , GLU B:110 , HIS B:135 , HOH B:1088	BINDING SITE FOR RESIDUE ABM B 1004

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

Asymmetric Unit

No.	Residues
1	Asp A:66	-	Pro A:67
2	Asp B:66	-	Pro B:67

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRPP_SYNTHASE	PS00114	Phosphoribosyl pyrophosphate synthase signature.	KPRS_BACSU	134-149	2	A:133-148 B:133-148

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRPP_SYNTHASE	PS00114	Phosphoribosyl pyrophosphate synthase signature.	KPRS_BACSU	134-149	2	A:133-148 B:133-148

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRPP_SYNTHASE	PS00114	Phosphoribosyl pyrophosphate synthase signature.	KPRS_BACSU	134-149	6	A:133-148 B:133-148

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRPP_SYNTHASE	PS00114	Phosphoribosyl pyrophosphate synthase signature.	KPRS_BACSU	134-149	2	A:133-148 B:133-148

(no "Exon" information available for 1DKU)

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:295
 aligned with KPRS_BACSU | P14193 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:308
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        
           KPRS_BACSU     9 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEQQSVSYLF 316
               SCOP domains d1dkua1 A:8-166 Phosphoribosylpyrophosphate synthetase                                                                                                         d1dkua2 A:167-315 Phosphoribosyl         pyrophosphate synthetase                                                                                     SCOP domains
               CATH domains 1dkuA02 A:8-151,A:293-315  [code=3.40.50.2020, no name defined]                                                                                 1dkuA01 A:152-292  [code=3.40.50.2020, no name          defined]                                                                             1dkuA02                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhh.....eeeee.....eeeee.......eeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.................hhhhhhhhhhhhhh..eeeee...hhhhhhhh...eeee.hhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh...eeeee..---------.eee......eeeee..ee..hhhhhhhhhhhhhh...eeeee..ee....hhhhhhhh..eeeeeee.....----....eeee.hhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------PRPP_SYNTHASE   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dku A   8 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRLKAPIAIIDKR---------MNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKL----KIERFKQLSVGPLLAEAIIRVHEQQSVSYLF 315
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197|        -|      217       227       237       247       257       267       277  |    287       297       307        
                                                                                                                                                                                                                        198       208                                                                     280  285

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with KPRS_BACSU | P14193 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:308
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        
           KPRS_BACSU     9 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEQQSVSYLF 316
               SCOP domains d1dkub1 B:8-166 Phosphoribosylpyrophosphate synthetase                                                                                                         d1dkub2 B:167-315 Phosphoribosyl         pyrophosphate synthetase                                                                                     SCOP domains
               CATH domains 1dkuB02 B:8-151,B:293-313  [code=3.40.50.2020, no name defined]                                                                                 1dkuB01 B:152-292  [code=3.40.50.2020, no name          defined]                                                                             1dkuB02              -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhh.....eeeee.....eeeee.......eeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee.................hhhhhhhhhhhhhh..eeeee...hhhhhhhh...eeee.hhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh..eeeee..---------.eee......eeeee..ee..hhhhhhhhhhhhhh...eeeee..ee....hhhhhhhh..eeeeeee.....----....eeee.hhhhhhhhhhhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------PRPP_SYNTHASE   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dku B   8 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRLKAPIAIIDKR---------MNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKL----KIERFKQLSVGPLLAEAIIRVHEQQSVSYLF 315
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197|        -|      217       227       237       247       257       267       277  |    287       297       307        
                                                                                                                                                                                                                        198       208                                                                     280  285

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: Phosphoribosylpyrophosphate synthetase-like (6)

Protein domain: Phosphoribosylpyrophosphate synthetase (5)

Bacillus subtilis [TaxId: 1423] (3)

1a	d1dkua1	A:8-166
1b	d1dkua2	A:167-315
1c	d1dkub1	B:8-166
1d	d1dkub2	B:167-315

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2020, no name defined] (117)

Bacillus subtilis. Organism_taxid: 1423. (2)

1a	1dkuA02	A:8-151,A:293-315
1b	1dkuB02	B:8-151,B:293-313
1c	1dkuA01	A:152-292
1d	1dkuB01	B:152-292

(no "Pfam Domain" information available for 1DKU)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KPRS_BACSU | P14193)

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:0044249	cellular biosynthetic process	The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
	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.

Asymmetric Unit
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	1dku
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	KPRS_BACSU \| P14193	:	1dkr 1ibs

1dkr	COMPLEX WITH SULFATE IONS BOUND IN THE ACTIVE AND ALLOSTERIC SITE

Description

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Ligands, Modified Residues, Ions (2, 4)

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Cis Peptide Bonds (2, 2)

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