4MIY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF MYO-INOSITOL DEHYDROGENASE FROM LACTOBACILLUS CASEI IN COMPLEX WITH NAD AND MYO-INOSITOL

Authors :   D. Bertwistle, D. A. R. Sanders, D. R. J. Palmer

Date :   02 Sep 13 (Deposition) - 04 Mar 15 (Release) - 04 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.42

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Nad, Sugar Alcohol Dehydrogenases, Rossmann Fold, Dehydrogenase, Nad Binding, Myo-Inositol Binding, Dehydrogenate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Bertwistle, H. Aamudalapalli, D. A. R. Sanders, D. R. J. Palmer
Crystal Structure Of Myo-Inositol Dehydrogenase From Lactobacillus Casei In Complex With Nad And Myo-Inositol
To Be Published
PubMed: search

Molecule 1 - INOSITOL 2-DEHYDROGENASE/D-CHIRO-INOSITOL 3-DEHYDROGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-80L
	Expression System Strain	:	XL1-BLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	IDH, IOLG, IOLG1, LCABL_02210
	Organism Scientific	:	LACTOBACILLUS CASEI
	Organism Taxid	:	543734
	Strain	:	BL23
	Synonym	:	MYO-INOSITOL 2-DEHYDROGENASE/D-CHIRO-INOSITOL 3- DEHYDROGENASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 24)

No.	Name	Count	Type	Full Name
1	GOL	12	Ligand/Ion	GLYCEROL
2	INS	1	Ligand/Ion	1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
3	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	SO4	7	Ligand/Ion	SULFATE ION

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:11 , ALA A:12 , MET A:13 , ASP A:35 , ILE A:36 , VAL A:73 , SER A:74 , PHE A:75 , HIS A:79 , GLU A:96 , LYS A:97 , GLY A:124 , HIS A:176 , TYR A:282 , HOH A:565 , HOH A:653 , HOH A:720 , HOH A:731 , HOH A:746	BINDING SITE FOR RESIDUE NAD A 401
02	AC2	SOFTWARE	ALA A:12 , MET A:13 , ALA A:16 , ILE A:275 , HOH A:579 , HOH A:731	BINDING SITE FOR RESIDUE GOL A 402
03	AC3	SOFTWARE	ARG A:152 , ALA A:153 , SER A:154 , GLU A:241 , HOH A:529 , ARG C:152 , GLU C:241	BINDING SITE FOR RESIDUE GOL A 403
04	AC4	SOFTWARE	HOH A:520 , LEU B:140 , ASP B:141 , GLY B:143 , GLY B:146 , PRO B:148 , HOH B:608 , HOH B:745	BINDING SITE FOR RESIDUE GOL A 404
05	AC5	SOFTWARE	THR A:26 , GLY A:27 , HOH A:577 , HOH A:682 , THR D:26 , GLY D:27	BINDING SITE FOR RESIDUE SO4 A 405
06	AC6	SOFTWARE	ARG A:198 , HOH A:542 , HOH A:708 , HOH A:711 , ALA C:147 , PRO C:148 , LYS C:220	BINDING SITE FOR RESIDUE SO4 A 406
07	AC7	SOFTWARE	GLY B:11 , ALA B:12 , MET B:13 , ASP B:35 , ILE B:36 , VAL B:73 , SER B:74 , PHE B:75 , ALA B:78 , HIS B:79 , GLU B:96 , LYS B:97 , GLY B:124 , MET B:126 , HIS B:176 , TYR B:282 , HOH B:607 , HOH B:615 , HOH B:620 , HOH B:632 , HOH B:638 , HOH B:698 , HOH B:729 , HOH B:753 , HOH B:760	BINDING SITE FOR RESIDUE NAD B 401
08	AC8	SOFTWARE	ALA B:12 , MET B:13 , ALA B:16 , ILE B:275 , HOH B:615 , HOH B:652	BINDING SITE FOR RESIDUE GOL B 402
09	AC9	SOFTWARE	GLN A:266 , THR A:268 , GLN B:266 , THR B:268	BINDING SITE FOR RESIDUE GOL B 403
10	BC1	SOFTWARE	THR B:26 , GLY B:27 , HOH B:743 , THR C:26 , GLY C:27	BINDING SITE FOR RESIDUE SO4 B 404
11	BC2	SOFTWARE	ARG B:198 , HOH B:606 , HOH B:747 , PRO D:148 , LYS D:220	BINDING SITE FOR RESIDUE SO4 B 405
12	BC3	SOFTWARE	GLY C:11 , ALA C:12 , MET C:13 , ASP C:35 , ILE C:36 , VAL C:73 , SER C:74 , PHE C:75 , GLY C:76 , ALA C:78 , HIS C:79 , GLU C:96 , LYS C:97 , GLY C:124 , HIS C:176 , TYR C:282 , HOH C:511 , HOH C:590 , HOH C:606 , HOH C:615 , HOH C:617 , HOH C:626 , HOH C:704 , HOH C:751 , HOH C:754	BINDING SITE FOR RESIDUE NAD C 401
13	BC4	SOFTWARE	ALA C:16 , HOH C:528 , HOH C:581 , HOH C:702 , ILE D:36 , ASP D:37 , HIS D:38 , HOH D:691	BINDING SITE FOR RESIDUE GOL C 402
14	BC5	SOFTWARE	ILE C:259 , GLN C:266 , THR C:268 , HOH C:774 , GLN D:266	BINDING SITE FOR RESIDUE GOL C 403
15	BC6	SOFTWARE	ARG A:152 , GLU A:241 , ARG C:152 , ALA C:153 , SER C:154 , GLU C:241 , HOH C:595	BINDING SITE FOR RESIDUE GOL C 404
16	BC7	SOFTWARE	HOH C:546 , HOH C:558 , HOH C:672 , HOH C:691 , HOH C:701	BINDING SITE FOR RESIDUE GOL C 405
17	BC8	SOFTWARE	ALA A:147 , LYS A:220 , ARG C:198 , HOH C:570	BINDING SITE FOR RESIDUE SO4 C 406
18	BC9	SOFTWARE	PHE C:75 , GLY C:76 , GLY C:77 , HOH C:624	BINDING SITE FOR RESIDUE SO4 C 407
19	CC1	SOFTWARE	GLY D:11 , ALA D:12 , MET D:13 , ASP D:35 , ILE D:36 , VAL D:73 , SER D:74 , PHE D:75 , ALA D:78 , HIS D:79 , GLU D:96 , LYS D:97 , MET D:126 , ASP D:172 , HIS D:176 , TRP D:274 , TYR D:282 , INS D:402 , HOH D:501 , HOH D:580 , HOH D:608 , HOH D:619 , HOH D:644 , HOH D:651 , HOH D:671 , HOH D:707 , HOH D:738 , HOH D:744 , HOH D:758 , HOH D:762	BINDING SITE FOR RESIDUE NAD D 401
20	CC2	SOFTWARE	LYS D:97 , HIS D:155 , ASN D:157 , ASP D:172 , THR D:173 , HIS D:176 , TYR D:236 , NAD D:401 , HOH D:517 , HOH D:549 , HOH D:651	BINDING SITE FOR RESIDUE INS D 402
21	CC3	SOFTWARE	ARG B:152 , GLU B:241 , ARG D:152 , ALA D:153 , SER D:154 , GLU D:241 , HOH D:532	BINDING SITE FOR RESIDUE GOL D 403
22	CC4	SOFTWARE	TYR D:129 , ARG D:134 , GLU D:288 , SO4 D:406 , HOH D:694 , HOH D:789 , HOH D:805	BINDING SITE FOR RESIDUE GOL D 404
23	CC5	SOFTWARE	ARG C:46 , SER D:162 , ASN D:163 , TYR D:164 , ASN D:205 , GLU D:206 , HOH D:535 , HOH D:734	BINDING SITE FOR RESIDUE GOL D 405
24	CC6	SOFTWARE	ARG D:134 , TRP D:183 , GOL D:404	BINDING SITE FOR RESIDUE SO4 D 406

(no "SS Bond" information available for 4MIY)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:97	-	Pro A:98
2	Asp A:210	-	Pro A:211
3	Lys B:97	-	Pro B:98
4	Asp B:210	-	Pro B:211
5	Lys C:97	-	Pro C:98
6	Asp C:210	-	Pro C:211
7	Lys D:97	-	Pro D:98
8	Asp D:210	-	Pro D:211

(no "SAP(SNP)/Variant" information available for 4MIY)

(no "PROSITE Motif" information available for 4MIY)

(no "Exon" information available for 4MIY)

Asymmetric/Biological 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:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh....ee..hhhhhh......eeee..hhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee..........hhhhhh.hhhhhhhhhhhhh..eeeeeee................eeeeeee....eeeeeee.......eeeeeeee...eee........eeee..eeeee...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4miy A   1 MVVKVGVIGTGAMGRAHIDRLTNVLTGAEVVAVTDIDHEAAEAAVRDFHLNAKVYPDDTSLLQDPDIDAVFVVSFGGAHEATVLKALDTDKFIFTEKPLATTLEGAKRIVDKELTKSKKVIQVGFMRRYDQGIRALKEKLDTGIIGAPLVVRASHINPNVASNYSNEMAITDTLIHEIDEMHWLLDDEYTSIQITYPRQSAEVRNEGLHDPQLATLTTKKGTVIQVLVHVTAQYGYEVKLEVIGETGELQLPNYGLGPILRSNANQQTAVEMSWINRFIQAYNTEVQEFIDEVAKSEPPVGPSAWDGYIAAITAAAANRSQKDQETVLINVAGTPTFYQ 339
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Chain B from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh....ee..hhhhhh......eeee..hhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee..........hhhhhh.hhhhhhhhhhhhh..eeeeeee................eeeeeee....eeeeeee.......eeeeeeee...eee........eeee..eeeee...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.....ee......hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4miy B   1 MVVKVGVIGTGAMGRAHIDRLTNVLTGAEVVAVTDIDHEAAEAAVRDFHLNAKVYPDDTSLLQDPDIDAVFVVSFGGAHEATVLKALDTDKFIFTEKPLATTLEGAKRIVDKELTKSKKVIQVGFMRRYDQGIRALKEKLDTGIIGAPLVVRASHINPNVASNYSNEMAITDTLIHEIDEMHWLLDDEYTSIQITYPRQSAEVRNEGLHDPQLATLTTKKGTVIQVLVHVTAQYGYEVKLEVIGETGELQLPNYGLGPILRSNANQQTAVEMSWINRFIQAYNTEVQEFIDEVAKSEPPVGPSAWDGYIAAITAAAANRSQKDQETVLINVAGTPTFYQ 339
                                    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       290       300       310       320       330

Chain C from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh....ee..hhhhhhh.....eeee..hhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhh......eeeeeeeee..........hhhhhh.hhhhhhhhhhhhh..eeeeeee................eeeeeee....eeeeeee.......eeeeeeee...eee........eeee..eeeee...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4miy C   1 MVVKVGVIGTGAMGRAHIDRLTNVLTGAEVVAVTDIDHEAAEAAVRDFHLNAKVYPDDTSLLQDPDIDAVFVVSFGGAHEATVLKALDTDKFIFTEKPLATTLEGAKRIVDKELTKSKKVIQVGFMRRYDQGIRALKEKLDTGIIGAPLVVRASHINPNVASNYSNEMAITDTLIHEIDEMHWLLDDEYTSIQITYPRQSAEVRNEGLHDPQLATLTTKKGTVIQVLVHVTAQYGYEVKLEVIGETGELQLPNYGLGPILRSNANQQTAVEMSWINRFIQAYNTEVQEFIDEVAKSEPPVGPSAWDGYIAAITAAAANRSQKDQETVLINVAGTPTFYQ 339
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Chain D from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh....ee..hhhhhhh.....eeee..hhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee..........hhhhhh.hhhhhhhhhhhhh..eeeeeee................eeeeeee....eeeeeee.......eeeeeeee...eee........eeee..eeeee...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4miy D   1 MVVKVGVIGTGAMGRAHIDRLTNVLTGAEVVAVTDIDHEAAEAAVRDFHLNAKVYPDDTSLLQDPDIDAVFVVSFGGAHEATVLKALDTDKFIFTEKPLATTLEGAKRIVDKELTKSKKVIQVGFMRRYDQGIRALKEKLDTGIIGAPLVVRASHINPNVASNYSNEMAITDTLIHEIDEMHWLLDDEYTSIQITYPRQSAEVRNEGLHDPQLATLTTKKGTVIQVLVHVTAQYGYEVKLEVIGETGELQLPNYGLGPILRSNANQQTAVEMSWINRFIQAYNTEVQEFIDEVAKSEPPVGPSAWDGYIAAITAAAANRSQKDQETVLINVAGTPTFYQ 339
                                    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       290       300       310       320       330

Legend:		→ Mismatch	(orange background)
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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 '\|'

(no "SCOP Domain" information available for 4MIY)

(no "CATH Domain" information available for 4MIY)

(no "Pfam Domain" information available for 4MIY)

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4MIY)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:210 - Pro A:211	[ RasMol ]
		Asp B:210 - Pro B:211	[ RasMol ]
		Asp C:210 - Pro C:211	[ RasMol ]
		Asp D:210 - Pro D:211	[ RasMol ]
		Lys A:97 - Pro A:98	[ RasMol ]
		Lys B:97 - Pro B:98	[ RasMol ]
		Lys C:97 - Pro C:98	[ RasMol ]
		Lys D:97 - Pro D:98	[ RasMol ]

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	4miy
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	A0A0J9X1Y2_L \| A0A0J9X1Y2
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UniProtKB/TrEMBL
	A0A0J9X1Y2_L \| A0A0J9X1Y2	:	4mie 4min 4mio 4mjl

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 24)

Sites (24, 24)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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