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Title :   CRYSTAL STRUCTURE OF THE 1L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE COMPLEXED WITH NADH

Authors :   X. Jin, J. H. Geiger

Date :   12 Apr 03 (Deposition) - 08 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   1L-Myo-Inositol 1-Phosphate, Nadh, Isomerase, Rossmann Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Jin, J. H. Geiger
Structures Of Nad(+)- And Nadh-Bound 1-L-Myo-Inositol 1-Phosphate Synthase.
Acta Crystallogr. , Sect. D V. 59 1154 2003
PubMed-ID: 12832758 | Reference-DOI: 10.1107/S0907444903008205

Molecule 1 - INOSITOL-3-PHOSPHATE SYNTHASE
	Chains	:	A, B
	EC Number	:	5.5.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	1L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE, MYO-INOSITOL-1- PHOSPHATE SYNTHASE, MI-1-P SYNTHASE, IPS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NAI	2	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NAI	4	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3	PO4	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:323 , GLY A:324 , GLN A:325 , THR A:326 , LYS A:373 , LYS A:412 , LYS A:489 , HOH A:2207	BINDING SITE FOR RESIDUE PO4 A 1700
2	AC2	SOFTWARE	SER B:323 , GLY B:324 , GLN B:325 , THR B:326 , LYS B:373 , LYS B:412 , LYS B:489 , GOL B:1311 , HOH B:1704	BINDING SITE FOR RESIDUE PO4 B 1701
3	AC3	SOFTWARE	ILE A:71 , GLY A:72 , GLY A:74 , GLY A:75 , ASN A:76 , ASN A:77 , ASP A:148 , ILE A:149 , SER A:184 , ILE A:185 , ARG A:198 , THR A:244 , ALA A:245 , ASN A:246 , THR A:247 , GLY A:295 , SER A:296 , ASP A:320 , LEU A:321 , SER A:323 , ASN A:355 , ASP A:356 , LYS A:369 , ASP A:438 , ALA A:442 , LYS A:489 , GOL A:1310 , HOH A:1726 , HOH A:1735 , HOH A:1762 , HOH A:1824 , HOH A:1864 , HOH A:2000 , HOH A:2238	BINDING SITE FOR RESIDUE NAI A 650
4	AC4	SOFTWARE	ILE B:71 , GLY B:72 , GLY B:74 , GLY B:75 , ASN B:76 , ASN B:77 , ASP B:148 , ILE B:149 , SER B:184 , ILE B:185 , ARG B:198 , THR B:244 , ALA B:245 , ASN B:246 , THR B:247 , GLY B:295 , SER B:296 , ASP B:320 , LEU B:321 , SER B:323 , ASN B:355 , ASP B:356 , LYS B:369 , ASP B:438 , ALA B:442 , LYS B:489 , GOL B:1311 , HOH B:1713 , HOH B:1745 , HOH B:1750 , HOH B:1902 , HOH B:1905 , HOH B:1908 , HOH B:2231	BINDING SITE FOR RESIDUE NAI B 660
5	AC5	SOFTWARE	ASN A:350 , ASP A:356 , LEU A:360 , LYS A:369 , LYS A:373 , ILE A:402 , LYS A:412 , ASP A:438 , NAI A:650	BINDING SITE FOR RESIDUE GOL A 1310
6	AC6	SOFTWARE	ASN B:350 , ASP B:356 , LYS B:369 , LYS B:373 , ILE B:402 , LYS B:412 , ASP B:438 , NAI B:660 , PO4 B:1701	BINDING SITE FOR RESIDUE GOL B 1311

(no "SS Bond" information available for 1P1J)

(no "Cis Peptide Bond" information available for 1P1J)

(no "SAP(SNP)/Variant" information available for 1P1J)

(no "PROSITE Motif" information available for 1P1J)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YJL153C	1	YJL153C.1	X:135929-134328	1602	INO1_YEAST	1-533	533	2	A:9-533 B:10-533 (gaps)	525 524

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:525
 aligned with INO1_YEAST | P11986 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:525
                                    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       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528     
           INO1_YEAST     9 ITSVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNHLGNNDGYNLSAPKQFRSKEISKSSVIDDIIASNDILYNDKLGKKVDHCIVIKYMKPVGDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDPVKEDAGKFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
               SCOP domains d1p1ja1 A:9-322,A:438-533 Myo-inositol 1-phosphate synthase                                                                                                                                                                                                                                                               d1p1ja2 A:323-437 Myo-inositol 1-phosphate synthase                                                                d1p1ja1 A:9-322,A:438-533 Myo-inositol 1-phosphate synthase                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....eeee..eeeeeeeeeeeeeee....eeeeeeeeeeeeeeee......eeeeee...hhhhhhhhhhhhhhhh...eee..eee......hhhhhheeeeee.....eeeee.hhh....hhh.eeeeee.....hhhhhhhhhh..hhhhhhhhhhhhh.........hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh....eeeee................hhhhhhhhhhh.....hhhhhhhhhhhhh...eee.......hhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeee.hhhh.eeeeeeeeeee.hhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhheeeee.................hhhhhhhh.............hhhhhhhhhhhhhhhhh........hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:9-533 UniProt: 1-533 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Transcript 1
                 1p1j A   9 ITSVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNHLGNNDGYNLSAPKQFRSKEISKSSVIDDIIASNDILYNDKLGKKVDHCIVIKYMKPVGDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDPVKEDAGKFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
                                    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       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528

Chain B from PDB  Type:PROTEIN  Length:516
 aligned with INO1_YEAST | P11986 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:524
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529    
           INO1_YEAST    10 TSVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNHLGNNDGYNLSAPKQFRSKEISKSSVIDDIIASNDILYNDKLGKKVDHCIVIKYMKPVGDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDPVKEDAGKFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
               SCOP domains d1p1jb1 B:10-322,B:438-533 Myo-inositol 1-phosphate synthase                                                                                                                                                                                                                                                             d1p1jb2 B:323-437 Myo-inositol 1-phosphate synthase                                                                d1p1jb1 B:10-322,B:438-533         Myo-inositol 1-phosphate synthase                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1p1jB02 B:323-437 Dihydrodipicolinate Reductase; domain 2                                                          ------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------------------------------------NAD_binding_5-1p1jB01 B:66-515                                                                                                                                                                                                                                                                                                                                                                                                                                    ------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------NAD_binding_5-1p1jB02 B:66-515                                                                                                                                                                                                                                                                                                                                                                                                                                    ------------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Inos-1-P_synth-1p1jB03 B:324-439                                                                                    ---------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Inos-1-P_synth-1p1jB04 B:324-439                                                                                    ---------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeee....eee...eeeeeeeeeeeeeee....eeeeeeeeeeeeeeee......eeeeee...hhhhhhhhhhhhhhhh.................hhhhhheeeeee.....eeeee.hhh....hhh.eeeeee.....hhhhhhhhhh..hhhhhhhhhhhhh.........hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhh...eeeee................hhhhhhhhhhh.....hhhhhhhhhhhhhh..eee.......hhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeee.hhhh.eeeeeeeeeee.hhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.eeeeee--------..ee....hhhhhhhh.............hhhhhhhhhhhhhhhhh........hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:10-533 (gaps) UniProt: 1-533 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Transcript 1
                 1p1j B  10 TSVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNHLGNNDGYNLSAPKQFRSKEISKSSVIDDIIASNDILYNDKLGKKVDHCIVIKYMKPVGDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKV--------KFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459    |    -   |   479       489       499       509       519       529    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                464      473

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: Dihydrodipicolinate Reductase; domain 2 (182)

Homologous Superfamily: Dihydrodipicolinate Reductase; domain 2 (178)

Baker's yeast (Saccharomyces cerevisiae) (12)

1p1jB02

B:323-437

Asymmetric Unit(hide GO term definitions)

Chain A,B (INO1_YEAST | P11986)

molecular function
	GO:0004512	inositol-3-phosphate synthase activity	Catalysis of the reaction: D-glucose 6-phosphate = 1D-myo-inositol 3-phosphate. This reaction requires NAD, which dehydrogenates the CHOH group to CO at C-5 of the glucose 6-phosphate, making C-6 into an active methylene, able to condense with the aldehyde at C-1. Finally, the enzyme-bound NADH reconverts C-5 into the CHOH form.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
	GO:0006021	inositol biosynthetic process	The chemical reactions and pathways resulting in the formation of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0008654	phospholipid biosynthetic process	The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
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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	Cis Peptide Bonds
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Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1p1j
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	5.5.1.4
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UniProtKB/Swiss-Prot
	INO1_YEAST \| P11986	:	1jkf 1jki 1la2 1p1f 1p1h 1p1i 1p1k 1rm0

1p1f	CRYSTAL STRUCTURE OF APO 1L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE
1p1h	CRYSTAL STRUCTURE OF 1L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE
1p1i	CRYSTAL STRUCTURE OF THE NAD+-BOUND 1L-MYO-INOSITOL 1- PHOSPHATE SYNTHASE
1p1k	CRYSTAL STRUCTURE OF THE 1L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE COMPLEXED WITH NADH AND EDTA

Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (1, 2)

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