1CLI - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE (PURM), FROM THE E. COLI PURINE BIOSYNTHETIC PATHWAY, AT 2.5 A RESOLUTION

Authors :   C. Li, T. J. Kappock, J. Stubbe, T. M. Weaver, S. E. Ealick

Date :   28 Apr 99 (Deposition) - 06 Oct 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: B,D  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B  (1x)
Biol. Unit 4: A,B,C,D  (1x)

Keywords :   Air Synthetase, Purm, Purine Biosynthesis, Trifunctional Enzyme, Purl, Fgar Amidotransferase, Novel Fold, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Li, T. J. Kappock, J. Stubbe, T. M. Weaver, S. E. Ealick
X-Ray Crystal Structure Of Aminoimidazole Ribonucleotide Synthetase (Purm), From The Escherichia Coli Purine Biosynthetic Pathway At 2. 5 A Resolution.
Structure Fold. Des. V. 7 1155 1999
PubMed-ID: 10508786 | Reference-DOI: 10.1016/S0969-2126(99)80182-8

Molecule 1 - PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
	Cellular Location	:	CYTOPLASM
	Chains	:	A, B, C, D
	EC Number	:	6.3.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Cell	:	BL21
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Cell Line	:	BL21
	Expression System Gene	:	PURM
	Expression System Plasmid	:	PJS119
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PET28
	Gene	:	PURM
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	SULFATE BINDNG
	Other Details - Source	:	CLONED GENE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:		B		D
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B
Biological Unit 4 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:69 , ASN A:192 , GLY A:193 , TYR A:194 , SER A:195 , HOH A:4420	BINDING SITE FOR RESIDUE SO4 A 4350
2	AC2	SOFTWARE	GLY B:1068 , THR B:1069 , ASN B:1192 , GLY B:1193 , TYR B:1194 , SER B:1195	BINDING SITE FOR RESIDUE SO4 B 1350
3	AC3	SOFTWARE	THR C:2069 , ASN C:2192 , GLY C:2193 , TYR C:2194 , SER C:2195	BINDING SITE FOR RESIDUE SO4 C 2350
4	AC4	SOFTWARE	GLY D:3068 , THR D:3069 , ASN D:3192 , GLY D:3193 , TYR D:3194 , SER D:3195	BINDING SITE FOR RESIDUE SO4 D 3350

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

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

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

(no "PROSITE Motif" information available for 1CLI)

(no "Exon" information available for 1CLI)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:341
 aligned with PUR5_ECOLI | P08178 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:341
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344 
          PUR5_ECOLI      5 TSLSYKDAGVDIDAGNALVGRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTASAVISGIAEGCLQSGCSLVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVSDGDVLIALGSSGPHSNGYSLVRKILEVSGCDPQTTELDGKPLADHLLAPTRIYVKSVLELIEKVDVHAIAHLTGGGFWENIPRVLPDNTQAVIDESSWQWPEVFNWLQTAGNVEHHEMYRTFNCGVGMIIALPAPEVDKALALLNANGENAWKIGIIKASDSEQRVVIE  345
               SCOP domains d1clia1 A:5-170 Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain                                                                                     d1clia2 A:171-345 Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain                                                                                             SCOP domains
               CATH domains 1cliA01 A:5-170  [code=3.30.1330.10, no name defined]                                                                                                                 1cliA02 A:171-345 Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhh.hhhhhhh.............eeee.......eeeeeeeee..hhhhhhhh......hhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhhhhhhh..eeeeeeeee.........eeeeeeeeeeeehhh...........eeeeee........hhhhhhhhhh..............hhhhhh......hhhhhhhhhh..eeeeee....hhhhhhhh.....eeeee.hhh....hhhhhhhhhh...hhhhhhh....eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee.....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1cli A    5 TSLSYKDAGVDIDAGNALVGRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTASAVISGIAEGCLQSGCSLVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVSDGDVLIALGSSGPHSNGYSLVRKILEVSGCDPQTTELDGKPLADHLLAPTRIYVKSVLELIEKVDVHAIAHLTGGGFWENIPRVLPDNTQAVIDESSWQWPEVFNWLQTAGNVEHHEMYRTFNCGVGMIIALPAPEVDKALALLNANGENAWKIGIIKASDSEQRVVIE  345
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344

Chain B from PDB  Type:PROTEIN  Length:325
 aligned with PUR5_ECOLI | P08178 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:325
                                    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       290       300       310       320       330       340     
          PUR5_ECOLI     21 ALVGRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTASAVISGIAEGCLQSGCSLVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVSDGDVLIALGSSGPHSNGYSLVRKILEVSGCDPQTTELDGKPLADHLLAPTRIYVKSVLELIEKVDVHAIAHLTGGGFWENIPRVLPDNTQAVIDESSWQWPEVFNWLQTAGNVEHHEMYRTFNCGVGMIIALPAPEVDKALALLNANGENAWKIGIIKASDSEQRVVIE  345
               SCOP domains d1clib1 B:1021-1170 Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain                                                                 d1clib2 B:1171-1345 Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain                                                                                           SCOP domains
               CATH domains 1cliB01 B:1021-1170  [code=3.30.1330.10, no name defined]                                                                                             1cliB02 B:1171-1345 Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.............eeee.......eeeeeeeee...hhhhhhh......hhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhhhhhhh..eeeeeeeee.........eeeeeeeeeeee..............eeeeee........hhhhhhhhhhh.............hhhhhh......hhhhhhhhhh..eeeeee....hhhhh.hhh....eeeee.hhh....hhhhhhhhhh...hhhhhhh....eeeeeee.hhhhhhhhhhhh.....eeeeeeeee......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1cli B 1021 ALVGRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTASAVISGIAEGCLQSGCSLVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVSDGDVLIALGSSGPHSNGYSLVRKILEVSGCDPQTTELDGKPLADHLLAPTRIYVKSVLELIEKVDVHAIAHLTGGGFWENIPRVLPDNTQAVIDESSWQWPEVFNWLQTAGNVEHHEMYRTFNCGVGMIIALPAPEVDKALALLNANGENAWKIGIIKASDSEQRVVIE 1345
                                  1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340

Chain C from PDB  Type:PROTEIN  Length:341
 aligned with PUR5_ECOLI | P08178 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:341
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344 
          PUR5_ECOLI      5 TSLSYKDAGVDIDAGNALVGRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTASAVISGIAEGCLQSGCSLVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVSDGDVLIALGSSGPHSNGYSLVRKILEVSGCDPQTTELDGKPLADHLLAPTRIYVKSVLELIEKVDVHAIAHLTGGGFWENIPRVLPDNTQAVIDESSWQWPEVFNWLQTAGNVEHHEMYRTFNCGVGMIIALPAPEVDKALALLNANGENAWKIGIIKASDSEQRVVIE  345
               SCOP domains d1clic1 C:2005-2170 Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain                                                                                 d1clic2 C:2171-2345 Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain                                                                                           SCOP domains
               CATH domains 1cliC01 C:2005-2170  [code=3.30.1330.10, no name defined]                                                                                                             1cliC02 C:2171-2345 Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh...............eeee.......eeeeeeeee...hhhhhhh......hhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhhhhhhh..eeeeeeeee.........eeeeeeeeeeee..............eeeeee........hhhhhhhhhh..............hhhhhh......hhhhhhhhhh..eeeeee....hhhhh.........eeee.hhh....hhhhhhhhhh...hhhh.......eeeeeee.hhhhhhhhhhhhhh...eeeeeeee......eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1cli C 2005 TSLSYKDAGVDIDAGNALVGRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTASAVISGIAEGCLQSGCSLVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVSDGDVLIALGSSGPHSNGYSLVRKILEVSGCDPQTTELDGKPLADHLLAPTRIYVKSVLELIEKVDVHAIAHLTGGGFWENIPRVLPDNTQAVIDESSWQWPEVFNWLQTAGNVEHHEMYRTFNCGVGMIIALPAPEVDKALALLNANGENAWKIGIIKASDSEQRVVIE 2345
                                  2014      2024      2034      2044      2054      2064      2074      2084      2094      2104      2114      2124      2134      2144      2154      2164      2174      2184      2194      2204      2214      2224      2234      2244      2254      2264      2274      2284      2294      2304      2314      2324      2334      2344

Chain D from PDB  Type:PROTEIN  Length:325
 aligned with PUR5_ECOLI | P08178 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:325
                                    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       290       300       310       320       330       340     
          PUR5_ECOLI     21 ALVGRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTASAVISGIAEGCLQSGCSLVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVSDGDVLIALGSSGPHSNGYSLVRKILEVSGCDPQTTELDGKPLADHLLAPTRIYVKSVLELIEKVDVHAIAHLTGGGFWENIPRVLPDNTQAVIDESSWQWPEVFNWLQTAGNVEHHEMYRTFNCGVGMIIALPAPEVDKALALLNANGENAWKIGIIKASDSEQRVVIE  345
               SCOP domains d1clid1 D:3021-3170 Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain                                                                 d1clid2 D:3171-3345 Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain                                                                                           SCOP domains
               CATH domains 1cliD01 D:3021-3170  [code=3.30.1330.10, no name defined]                                                                                             1cliD02 D:3171-3345 Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh.............eeee.......eeeeeeeee...hhhhhhh......hhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhhhhhhh..eeee..eee.........eeeeeeeeeeeehhh...........eeeeee........hhhhhhhhhhh.............hhhhh.......hhhhhhhhhh..eeeeee....hhhhh.hhh....eeeee........hhhhhhhhh....hhhhhhh....eeeeeee.hhhhhhhhhhhhh....eeeeeeeee......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1cli D 3021 ALVGRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTASAVISGIAEGCLQSGCSLVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVSDGDVLIALGSSGPHSNGYSLVRKILEVSGCDPQTTELDGKPLADHLLAPTRIYVKSVLELIEKVDVHAIAHLTGGGFWENIPRVLPDNTQAVIDESSWQWPEVFNWLQTAGNVEHHEMYRTFNCGVGMIIALPAPEVDKALALLNANGENAWKIGIIKASDSEQRVVIE 3345
                                  3030      3040      3050      3060      3070      3080      3090      3100      3110      3120      3130      3140      3150      3160      3170      3180      3190      3200      3210      3220      3230      3240      3250      3260      3270      3280      3290      3300      3310      3320      3330      3340

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.10, no name defined] (8)

Escherichia coli. Organism_taxid: 562. (1)

1a	1cliB01	B:1021-1170
1b	1cliD01	D:3021-3170
1c	1cliA01	A:5-170
1d	1cliC01	C:2005-2170

Architecture: Alpha-Beta Complex (3881)

Topology: Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 (8)

Homologous Superfamily: Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 (8)

Escherichia coli. Organism_taxid: 562. (1)

2a	1cliA02	A:171-345
2b	1cliB02	B:1171-1345
2c	1cliC02	C:2171-2345
2d	1cliD02	D:3171-3345

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PUR5_ECOLI | P08178)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar 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.
	GO:0004641	phosphoribosylformylglycinamidine cyclo-ligase activity	Catalysis of the reaction: 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-D-ribosyl)imidazole + ADP + 2 H(+) + phosphate.
biological process
	GO:0006189	'de novo' IMP biosynthetic process	The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of 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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

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