1OX6 - JenaLib

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Title :   TOWARDS UNDERSTANDING THE MECHANISM OF THE COMPLEX CYCLIZATION REACTION CATALYZED BY IMIDAZOLE GLYCEROPHOSPHATE SYNTHASE

Authors :   B. N. Chaudhuri, J. L. Smith

Date :   01 Apr 03 (Deposition) - 17 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Complex Cyclization; Imidazole Glycerophosphate Synthase, Transferase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. N. Chaudhuri, S. C. Lange, R. S. Myers, V. J. Davisson, J. L. Smith
Towards Understanding The Mechanism Of The Complex Cyclization Reaction Catalyzed By Imidazole Glycerophosphate Synthase: Crystal Structures Of A Ternary Complex And The Free Enzyme
Biochemistry V. 42 7003 2003
PubMed-ID: 12795595 | Reference-DOI: 10.1021/BI034320H
(for further references see the PDB file header)

Molecule 1 - IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE HISHF
	Chains	:	A, B
	EC Number	:	2.4.2.-, 4.1.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	AMIDOTRANSFERASE AND CYCLASE DOMAINS
	Gene	:	HIS7
	Glutamine Amidotransferase	:	CYCLASE
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	HISTIDINE BIOSYNTHESIS BIFUNCTIONAL AMIDOTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	NI	2	Ligand/Ion	NICKEL (II) ION
2	POP	1	Ligand/Ion	PYROPHOSPHATE 2-
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	POP	-1	Ligand/Ion	PYROPHOSPHATE 2-
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	POP	1	Ligand/Ion	PYROPHOSPHATE 2-
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:-3 , SER B:-2 , HIS B:-1 , MET B:1	BINDING SITE FOR RESIDUE NI B 901
2	AC2	SOFTWARE	HIS A:-1 , GLY A:-3 , SER A:-2 , MET A:1 , TYR B:425	BINDING SITE FOR RESIDUE NI A 902
3	AC3	SOFTWARE	GLY A:364 , THR A:365	BINDING SITE FOR RESIDUE SO4 A 801
4	AC4	SOFTWARE	GLY A:475 , SER A:500 , GLY A:501 , HOH A:961 , HOH A:1034	BINDING SITE FOR RESIDUE SO4 A 802
5	AC5	SOFTWARE	LYS B:158 , LYS B:170 , LYS B:343	BINDING SITE FOR RESIDUE SO4 B 803
6	AC6	SOFTWARE	GLY B:331 , GLY B:364 , THR B:365 , HOH B:1107 , HOH B:1126	BINDING SITE FOR RESIDUE SO4 B 804
7	AC7	SOFTWARE	SER A:130 , ASN A:132 , HOH A:1027 , LYS B:493	BINDING SITE FOR RESIDUE SO4 A 806
8	AC8	SOFTWARE	ASP B:474 , GLY B:475 , ASN B:477 , SER B:500 , GLY B:501 , GLY B:524 , MET B:525 , ARG B:528 , HOH B:1013 , HOH B:1050 , HOH B:1095	BINDING SITE FOR RESIDUE POP B 999

(no "SS Bond" information available for 1OX6)

Asymmetric Unit

No.	Residues
1	Val A:119	-	Pro A:120
2	Val B:119	-	Pro B:120

(no "SAP(SNP)/Variant" information available for 1OX6)

(no "PROSITE Motif" information available for 1OX6)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YBR248C	1	YBR248C.1	II:716460-714802	1659	HIS5_YEAST	1-552	552	2	A:1-550 (gaps) B:1-550 (gaps)	550 550

Asymmetric Unit

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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
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Chain A from PDB  Type:PROTEIN  Length:531
 aligned with HIS5_YEAST | P33734 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:553
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547   
           HIS5_YEAST     - ---MPVVHVIDVESGNLQSLTNAIEHLGYEVQLVKSPKDFNISGTSRLILPGVGNYGHFVDNLFNRGFEKPIREYIESGKPIMGICVGLQALFAGSVESPKSTGLNYIDFKLSRFDDSEKPVPEIGWNSCIPSENLFFGLDPYKRYYFVHSFAAILNSEKKKNLENDGWKIAKAKYGSEEFIAAVNKNNIFATQFHPEKSGKAGLNVIENFLKQQSPPIPNYSAEEKELLMNDYSNYGLTRRIIACLDVRTNDQGDLVVTKGDQYDVREKSDGKGVRNLGKPVQLAQKYYQQGADEVTFLNITSFRDCPLKDTPMLEVLKQAAKTVFVPLTVGGGIKDIVDVDGTKIPALEVASLYFRSGADKVSIGTDAVYAAEKYYELGNRGDGTSPIETISKAYGAQAVVISVDPKRVYVNSQADTKNKVFETEYPGPNGEKYCWYQCTIKGGRESRDLGVWELTRACEALGAGEILLNCIDKDGSNSGYDLELIEHVKDAVKIPVIASSGAGVPEHFEEAFLKTRADACLGAGMFHRGEFTVNDVKEYLLEHGLKVRMD 550
               SCOP domains d1ox6a2 A:-3-229 GAT subunit, HisH, (or domain) of imidazoleglycerolphosphate synthase HisF                                                                                                                                             d1ox6a1 A:230-550 Cyclase s                   ubunit (or domain) of imi   dazoleglycerolphosphate synthase HisF                                                                                                                                                                                                                   SCOP domains
               CATH domains 1ox6A01 A:-3-237  [code=3.40.50.880, no name defined]                                                                                                                                                                                           1ox6A02 A:238-550 A                   ldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .....eeeee.......hhhhhhhhh...eeeee..hhh..hhh...eeeee...hhhhhhhhhh..hhhhhhhhhhh...----hhhhhhh....hhh........................eeeee.................eeeee.......hhhhhhhhh...eeeeeee..eeeeeeeee..eeee...hhh.hhhhhhhhhhhhh..........hhhhhhh....hhhh...eeeeeeeee.........-------------------.hhhhhhhhhhhh....eeeeeee.---...hhh.hhhhhhhhhhh....eeeee...............hhhhhhhhhhh...eeee.hhhhhhhhhhhh.........hhhhhhhhh.hhheeeeeeeeeeee..hhh.................eeeeee............hhhhhhhhhhh...eeeeee...........hhhhhhhhhh...eeee......hhhhhhhhhh....eeee.hhhh.....hhhhhhhhhhh....... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------eeeee----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 ---Exon 1.1  PDB: A:1-550 (gaps) UniProt: 1-552 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Transcript 1
                 1ox6 A  -3 GSHMPVVHVIDVESGNLQSLTNAIEHLGYEVQLVKSPKDFNISGTSRLILPGVGNYGHFVDNLFNRGFEKPIREYIESGKPIMGICVGLQALFAGSVESPKSTGLNYIDFKLSRFDDSEKPVPEIGWNSCIPSENLFFGLDPYKRYYFVHSFAAILNSEKKKNLENDGWKIAKAKYGSEEFIAAVNKNNIFATQFHPEKSGKAGLNVIENFLKQQSPPIPNYSAEEKELLMNDYSNYGLTRRIIACLDVRTNDQGDLVV-------------------LGKPVQLAQKYYQQGADEVTFLNIT---DCPLKDTPMLEVLKQAAKTVFVPLTVGGGIKDIVDVDGTKIPALEVASLYFRSGADKVSIGTDAVYAAEKYYELGNRGDGTSPIETISKAYGAQAVVISVDPKRVYVNSQADTKNKVFETEYPGPNGEKYCWYQCTIKGGRESRDLGVWELTRACEALGAGEILLNCIDKDGSNSGYDLELIEHVKDAVKIPVIASSGAGVPEHFEEAFLKTRADACLGAGMFHRGEFTVNDVKEYLLEHGLKVRMD 550
                              ||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247        |-         -       277       287       297  |   |307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547   
                             -1|                                                                                                                                                                                                                                                            256                 276                     300 304                                                                                                                                                                                                                                                      
                               1

Chain B from PDB  Type:PROTEIN  Length:531
 aligned with HIS5_YEAST | P33734 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:553
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547   
           HIS5_YEAST     - ---MPVVHVIDVESGNLQSLTNAIEHLGYEVQLVKSPKDFNISGTSRLILPGVGNYGHFVDNLFNRGFEKPIREYIESGKPIMGICVGLQALFAGSVESPKSTGLNYIDFKLSRFDDSEKPVPEIGWNSCIPSENLFFGLDPYKRYYFVHSFAAILNSEKKKNLENDGWKIAKAKYGSEEFIAAVNKNNIFATQFHPEKSGKAGLNVIENFLKQQSPPIPNYSAEEKELLMNDYSNYGLTRRIIACLDVRTNDQGDLVVTKGDQYDVREKSDGKGVRNLGKPVQLAQKYYQQGADEVTFLNITSFRDCPLKDTPMLEVLKQAAKTVFVPLTVGGGIKDIVDVDGTKIPALEVASLYFRSGADKVSIGTDAVYAAEKYYELGNRGDGTSPIETISKAYGAQAVVISVDPKRVYVNSQADTKNKVFETEYPGPNGEKYCWYQCTIKGGRESRDLGVWELTRACEALGAGEILLNCIDKDGSNSGYDLELIEHVKDAVKIPVIASSGAGVPEHFEEAFLKTRADACLGAGMFHRGEFTVNDVKEYLLEHGLKVRMD 550
               SCOP domains d1ox6b2 B:-3-229 GAT subunit, HisH, (or domain) of imidazoleglycerolphosphate synthase HisF                                                                                                                                             d1ox6b1 B:230-550 Cyclase s                   ubunit (or domain) of imi   dazoleglycerolphosphate synthase HisF                                                                                                                                                                                                                   SCOP domains
               CATH domains 1ox6B01 B:-3-237  [code=3.40.50.880, no name defined]                                                                                                                                                                                           1ox6B02 B:238-550 A                   ldolase class I                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -------GATase-1ox6B01 B:5-212                                                                                                                                                                                          --------------------------His_biosynth-1ox6B                   03 B:239-532                                                                                                                                                                                                                                                     ------------------ Pfam domains (1)
           Pfam domains (2) -------GATase-1ox6B02 B:5-212                                                                                                                                                                                          --------------------------His_biosynth-1ox6B                   04 B:239-532                                                                                                                                                                                                                                                     ------------------ Pfam domains (2)
     Sec.struct. author (1) ......eeee.......hhhhhhhhh....eeee..hhh..hhh...eeeee...hhhhhhhhhh..hhhhhhhhhhh...----hhhhhhh....hhh........................eeeee.................eeeee.......hhhhhhhhh...eeeeeee..eeeeeeeee..eeee...hhh.hhhhhhhhhhhh...........hhhhhhh....hhhh....eeeeeee..........-------------------.hhhhhhhhhhhh....eeeeee..---...hhh.hhhhhhhhhhh....eeeee...............hhhhhhhhhhh...eeee.hhhhhhhhhhhh.........hhhhhhhhh.hhheeeeeeeeeeee..hhh.................eeeeee............hhhhhhhhhhh...eeeeee...........hhhhhhhhhh...eeee......hhhhhhhhhh.....eee.hhhh.....hhhhhhhhhhh....... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------eeeee----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 ---Exon 1.1  PDB: B:1-550 (gaps) UniProt: 1-552 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Transcript 1
                 1ox6 B  -3 GSHMPVVHVIDVESGNLQSLTNAIEHLGYEVQLVKSPKDFNISGTSRLILPGVGNYGHFVDNLFNRGFEKPIREYIESGKPIMGICVGLQALFAGSVESPKSTGLNYIDFKLSRFDDSEKPVPEIGWNSCIPSENLFFGLDPYKRYYFVHSFAAILNSEKKKNLENDGWKIAKAKYGSEEFIAAVNKNNIFATQFHPEKSGKAGLNVIENFLKQQSPPIPNYSAEEKELLMNDYSNYGLTRRIIACLDVRTNDQGDLVV-------------------LGKPVQLAQKYYQQGADEVTFLNIT---DCPLKDTPMLEVLKQAAKTVFVPLTVGGGIKDIVDVDGTKIPALEVASLYFRSGADKVSIGTDAVYAAEKYYELGNRGDGTSPIETISKAYGAQAVVISVDPKRVYVNSQADTKNKVFETEYPGPNGEKYCWYQCTIKGGRESRDLGVWELTRACEALGAGEILLNCIDKDGSNSGYDLELIEHVKDAVKIPVIASSGAGVPEHFEEAFLKTRADACLGAGMFHRGEFTVNDVKEYLLEHGLKVRMD 550
                              ||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247        |-         -       277       287       297  |   |307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547   
                             -1|                                                                                                                                                                                                                                                            256                 276                     300 304                                                                                                                                                                                                                                                      
                               1

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.880, no name defined] (97)

Baker's yeast (Saccharomyces cerevisiae) (8)

1a	1ox6A01	A:-3-237
1b	1ox6B01	B:-3-237

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Baker's yeast (Saccharomyces cerevisiae) (49)

2a	1ox6A02	A:238-550
2b	1ox6B02	B:238-550

Asymmetric Unit(hide GO term definitions)

Chain A,B (HIS5_YEAST | P33734)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004359	glutaminase activity	Catalysis of the reaction: L-glutamine + H2O = L-glutamate + NH3.
	GO:0000107	imidazoleglycerol-phosphate synthase activity	Catalysis of the reaction: phosphoribulosylformimino-AICAR-P + L-glutamine = D-erythro-imidazole-glycerol-phosphate + aminoimidazole carboxamide ribonucleotide + L-glutamate + 2 H(+).
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0016833	oxo-acid-lyase activity	Catalysis of the cleavage of a C-C bond by other means than by hydrolysis or oxidation, of a 3-hydroxy acid.
	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.
	GO:0016763	transferase activity, transferring pentosyl groups	Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0006541	glutamine metabolic process	The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
	GO:0000105	histidine biosynthetic process	The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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.

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	HIS5_YEAST \| P33734	:	1jvn 1ox4 1ox5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (1, 2)

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