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Title :   CRYSTAL STRUCTURE OF HUMAN MYO-INOSITOL OXYGENASE (MIOX)

Authors :   B. M. Hallberg, R. D. Busam, C. Arrowsmith, H. Berglund, R. Collins, A. Edwards, M. Ehn, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, M. Hogbom, L. Holmberg-Schiavone, I. Johansson, T. Karlberg, T. Kotenyova, P. Nilsson-Ehle, P. Nordlund, T. Nyman, D. Ogg, J. Sagemark, P. Stenmark, M. Sundstrom, J. Uppenberg, S. Van Den Berg, J. Weigelt, A. G. Thorsell, C. Persson, Structural Genomics Consortium (Sgc)

Date :   11 Sep 06 (Deposition) - 17 Oct 06 (Release) - 17 Jun 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Reductase, Inositol, Diiron, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. G. Thorsell, C. Persson, N. Voevodskaya, R. D. Busam, M. Hammarstrom, S. Graslund, A. Graslund, B. M. Hallberg
Structural And Biophysical Characterization Of Human Myo-Inositol Oxygenase
J. Biol. Chem. V. 283 15209 2008
PubMed-ID: 18364358 | Reference-DOI: 10.1074/JBC.M800348200
(for further references see the PDB file header)

Molecule 1 - INOSITOL OXYGENASE
	Chains	:	A, B
	EC Number	:	1.13.99.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MYO-INOSITOL OXYGENASE, ALDEHYDE REDUCTASE-LIKE 6, RENAL-SPECIFIC OXIDOREDUCTASE, KIDNEY-SPECIFIC PROTEIN 32

		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 (5, 30)

No.	Name	Count	Type	Full Name
1	CYS	2	Mod. Amino Acid	CYSTEINE
2	FE	4	Ligand/Ion	FE (III) ION
3	I1N	2	Ligand/Ion	(2S,3R,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXANONE
4	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 13)

No.	Name	Count	Type	Full Name
1	CYS	1	Mod. Amino Acid	CYSTEINE
2	FE	-1	Ligand/Ion	FE (III) ION
3	I1N	1	Ligand/Ion	(2S,3R,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXANONE
4	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 13)

No.	Name	Count	Type	Full Name
1	CYS	1	Mod. Amino Acid	CYSTEINE
2	FE	-1	Ligand/Ion	FE (III) ION
3	I1N	1	Ligand/Ion	(2S,3R,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXANONE
4	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:98 , HIS A:123 , ASP A:124 , ASP A:253 , HOH A:737 , HOH A:812	BINDING SITE FOR RESIDUE FE A 703
02	AC2	SOFTWARE	ASP A:124 , HIS A:194 , HIS A:220 , I1N A:710 , HOH A:812	BINDING SITE FOR RESIDUE FE A 704
03	AC3	SOFTWARE	HIS B:98 , HIS B:123 , ASP B:124 , ASP B:253 , HOH B:782 , HOH B:807	BINDING SITE FOR RESIDUE FE B 705
04	AC4	SOFTWARE	ASP B:124 , HIS B:194 , HIS B:220 , I1N B:709 , HOH B:807	BINDING SITE FOR RESIDUE FE B 706
05	AC5	SOFTWARE	ARG A:229 , ARG A:247 , HOH A:929 , HOH A:962	BINDING SITE FOR RESIDUE SO4 A 701
06	AC6	SOFTWARE	ARG B:229 , HOH B:845 , HOH B:889 , HOH B:945 , HOH B:971	BINDING SITE FOR RESIDUE SO4 B 702
07	AC7	SOFTWARE	ASP A:85 , SER A:87 , ASP A:124 , LYS A:127 , VAL A:140 , GLY A:141 , ASP A:142 , HIS A:194 , HIS A:220 , SER A:221 , TYR A:223 , FE A:704 , HOH A:737 , HOH A:755 , HOH A:812	BINDING SITE FOR RESIDUE I1N A 710
08	AC8	SOFTWARE	ASP B:85 , SER B:87 , ASP B:124 , LYS B:127 , VAL B:140 , GLY B:141 , ASP B:142 , HIS B:194 , HIS B:220 , SER B:221 , FE B:706 , HOH B:782 , HOH B:807 , HOH B:972	BINDING SITE FOR RESIDUE I1N B 709
09	AC9	SOFTWARE	ASP B:112 , LYS B:113 , TRP B:225 , ARG B:229 , GLN B:232 , CYS B:235 , SER B:236 , HOH B:744 , HOH B:929	BINDING SITE FOR RESIDUE CYS B 707
10	BC1	SOFTWARE	ASP A:112 , LYS A:113 , TRP A:225 , ARG A:229 , GLN A:232 , CYS A:235 , SER A:236 , HOH A:715 , HOH A:927	BINDING SITE FOR RESIDUE CYS A 708

(no "SS Bond" information available for 2IBN)

(no "Cis Peptide Bond" information available for 2IBN)

(no "SAP(SNP)/Variant" information available for 2IBN)

(no "PROSITE Motif" information available for 2IBN)

Asymmetric Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000216075	1b	ENSE00001944909	chr22:50925253-50925341	89	MIOX_HUMAN	1-5	5	0	-	-
1.2	ENST00000216075	2	ENSE00000878900	chr22:50925814-50925894	81	MIOX_HUMAN	6-32	27	0	-	-
1.3	ENST00000216075	3	ENSE00000657697	chr22:50926091-50926171	81	MIOX_HUMAN	33-59	27	2	A:36-59 (gaps) B:36-59 (gaps)	27 27
1.4	ENST00000216075	4	ENSE00000657699	chr22:50926315-50926477	163	MIOX_HUMAN	60-114	55	2	A:60-114 (gaps) B:60-114 (gaps)	55 55
1.5b	ENST00000216075	5b	ENSE00000657701	chr22:50926704-50926771	68	MIOX_HUMAN	114-136	23	2	A:114-136 B:114-136	23 23
1.6a	ENST00000216075	6a	ENSE00001774113	chr22:50927469-50927578	110	MIOX_HUMAN	137-173	37	2	A:137-173 B:137-173	37 37
1.7	ENST00000216075	7	ENSE00001736525	chr22:50927657-50927724	68	MIOX_HUMAN	173-196	24	2	A:173-196 B:173-196	24 24
1.8	ENST00000216075	8	ENSE00000657708	chr22:50927826-50927875	50	MIOX_HUMAN	196-212	17	2	A:196-212 B:196-212	17 17
1.9b	ENST00000216075	9b	ENSE00000657711	chr22:50927961-50928073	113	MIOX_HUMAN	213-250	38	2	A:213-250 B:213-250	38 38
1.10c	ENST00000216075	10c	ENSE00001690311	chr22:50928177-50928483	307	MIOX_HUMAN	250-285	36	2	A:250-285 (gaps) B:250-285 (gaps)	36 36

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
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Chain A from PDB  Type:PROTEIN  Length:241
 aligned with MIOX_HUMAN | Q9UGB7 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:253
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282   
           MIOX_HUMAN    33 SGPLLDRVFTTYKLMHTHQTVDFVRSKHAQFGGFSYKKMTVMEAVDLLDGLVDESDPDVDFPNSFHAFQTAEGIRKAHPDKDWFHLVGLLHDLGKVLALFGEPQWAVVGDTFPVGCRPQASVVFCDSTFQDNPDLQDPRYSTELGMYQPHCGLDRVLMSWGHDEYMYQVMKFNKFSLPPEAFYMIRFHSFYPWHTGRDYQQLCSQQDLAMLPWVREFNKFDLYTKCPDLPDVDKLRPYYQGLIDKYCPGILSW 285
               SCOP domains -   d2ibna1 A:37-285 Myo-inositol oxygenase MioX                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhh.....---..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhh................hhhhhh..hhhhhh..............hhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhh------..hhhhhhhhhhhhhhhhh...eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3 UniProt: 33-59    Exon 1.4  PDB: A:60-114 (gaps) UniProt: 60-114         ----------------------Exon 1.6a  PDB: A:137-173            ----------------------Exon 1.8         -------------------------------------Exon 1.10c  PDB: A:250-285 (gaps)    Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------Exon 1.5b              ------------------------------------Exon 1.7  PDB: A:173-196----------------Exon 1.9b  PDB: A:213-250             ----------------------------------- Transcript 1 (2)
                 2ibn A  36 S---mDRVFTTYKLmHTHQTVDFVRSKHAQFGGFSYKKmTVmEAVDLLDGLVDESD---DFPNSFHAFQTAEGIRKAHPDKDWFHLVGLLHDLGKVLALFGEPQWAVVGDTFPVGCRPQASVVFCDSTFQDNPDLQDPRYSTELGmYQPHCGLDRVLmSWGHDEYmYQVmKFNKFSLPPEAFYmIRFHSFYPWHTGRDYQQLCSQQDLAmLPWVREFNKFDL------LPDVDKLRPYYQGLIDKYCPGILSW 285
                            |   |   42    |   52        62        72 |      82     |  92       102       112       122       132       142       152       162       172     | 182       192     | 202       212   |   222       232       242       252 |     262       272       282   
                            |   |        47-MSE                  71-MSE           88  92                                                                                   178-MSE     190-MSE 198-MSE           216-MSE                   242-MSE     254    261                        
                           36   |                                   74-MSE                                                                                                                         202-MSE                                                                               
                               37-MSE

Chain B from PDB  Type:PROTEIN  Length:235
 aligned with MIOX_HUMAN | Q9UGB7 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:253
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282   
           MIOX_HUMAN    33 SGPLLDRVFTTYKLMHTHQTVDFVRSKHAQFGGFSYKKMTVMEAVDLLDGLVDESDPDVDFPNSFHAFQTAEGIRKAHPDKDWFHLVGLLHDLGKVLALFGEPQWAVVGDTFPVGCRPQASVVFCDSTFQDNPDLQDPRYSTELGMYQPHCGLDRVLMSWGHDEYMYQVMKFNKFSLPPEAFYMIRFHSFYPWHTGRDYQQLCSQQDLAMLPWVREFNKFDLYTKCPDLPDVDKLRPYYQGLIDKYCPGILSW 285
               SCOP domains d   2ibnb_ B: Myo-inositol oxygenase MioX                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhh....------hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhh................hhhhhh..hhhhh...............hhhhh....hhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhh.---------...hhhhhhhhhhhhh...eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3 UniProt: 33-59    Exon 1.4  PDB: B:60-114 (gaps) UniProt: 60-114         ----------------------Exon 1.6a  PDB: B:137-173            ----------------------Exon 1.8         -------------------------------------Exon 1.10c  PDB: B:250-285 (gaps)    Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------Exon 1.5b              ------------------------------------Exon 1.7  PDB: B:173-196----------------Exon 1.9b  PDB: B:213-250             ----------------------------------- Transcript 1 (2)
                 2ibn B  36 S---mDRVFTTYKLmHTHQTVDFVRSKHAQFGGFSYKKmTVmEAVDLLDGLVDES------PNSFHAFQTAEGIRKAHPDKDWFHLVGLLHDLGKVLALFGEPQWAVVGDTFPVGCRPQASVVFCDSTFQDNPDLQDPRYSTELGmYQPHCGLDRVLmSWGHDEYmYQVmKFNKFSLPPEAFYmIRFHSFYPWHTGRDYQQLCSQQDLAmLPWVREFNKFDL---------VDKLRPYYQGLIDKYCPGILSW 285
                            |   |   42    |   52        62        72 |      82    |    - |     102       112       122       132       142       152       162       172     | 182       192     | 202       212   |   222       232       242       252 |       - |     272       282   
                           36   |        47-MSE                  71-MSE          87     94                                                                                 178-MSE     190-MSE 198-MSE           216-MSE                   242-MSE     254       264                     
                               37-MSE                               74-MSE                                                                                                                         202-MSE

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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(

)

Folds(

)

Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: HD-domain/PDEase-like (204)

Superfamily: HD-domain/PDEase-like (204)

Family: MioX-like (3)

Protein domain: Myo-inositol oxygenase MioX (3)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2ibna1	A:37-285
1b	d2ibnb_	B:

(no "CATH Domain" information available for 2IBN)

(no "Pfam Domain" information available for 2IBN)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MIOX_HUMAN | Q9UGB7)

molecular function
	GO:0004033	aldo-keto reductase (NADP) activity	Catalysis of the reaction: an alcohol + NADP+ = an aldehyde or a ketone + NADPH + H+.
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0050113	inositol oxygenase activity	Catalysis of the reaction: myo-inositol + O(2) = D-glucuronate + H(2)O + H(+).
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016651	oxidoreductase activity, acting on NAD(P)H	Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0016701	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and molecular oxygen is incorporated into a donor.
biological process
	GO:0019310	inositol catabolic process	The chemical reactions and pathways resulting in the breakdown of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016234	inclusion body	A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers.

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