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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   SULFITE OXIDASE FROM CHICKEN LIVER

Authors :   C. Kisker, H. Schindelin, D. C. Rees

Date :   31 Dec 97 (Deposition) - 29 Apr 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Oxidoreductase, Sulfite Oxidation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Kisker, H. Schindelin, A. Pacheco, W. A. Wehbi, R. M. Garrett, K. V. Rajagopalan, J. H. Enemark, D. C. Rees
Molecular Basis Of Sulfite Oxidase Deficiency From The Structure Of Sulfite Oxidase.
Cell(Cambridge, Mass. ) V. 91 973 1997
PubMed-ID: 9428520 | Reference-DOI: 10.1016/S0092-8674(00)80488-2

Molecule 1 - SULFITE OXIDASE
	Cellular Location	:	MITOCHONDRIAL INTERMEMBRANE SPACE
	Chains	:	A, B
	EC Number	:	1.8.3.1
	Organ	:	LIVER
	Organelle	:	MITOCHONDRION
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 12)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	MO	2	Ligand/Ion	MOLYBDENUM ATOM
5	MTE	2	Ligand/Ion	PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
6	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:138 , CYS A:185 , GLY A:187 , ARG A:190 , GLY A:201 , LEU A:202 , TRP A:204 , TYR A:322 , ARG A:450 , HOH A:913 , HOH A:1147	BINDING SITE FOR RESIDUE SO4 A 503
02	AC2	SOFTWARE	HIS A:140 , TRP A:317 , HOH A:984 , HOH A:1132 , HOH A:1181 , HOH A:1206 , ARG B:337 , HOH B:1204 , HOH B:1298	BINDING SITE FOR RESIDUE SO4 A 504
03	AC3	SOFTWARE	ARG B:138 , CYS B:185 , ARG B:190 , GLY B:201 , LEU B:202 , TRP B:204 , TYR B:322 , ARG B:450 , HOH B:912 , HOH B:913	BINDING SITE FOR RESIDUE SO4 B 503
04	AC4	SOFTWARE	ARG A:337 , HIS B:140 , TRP B:317 , HOH B:953 , HOH B:1079 , HOH B:1138 , HOH B:1310	BINDING SITE FOR RESIDUE SO4 B 504
05	AC5	SOFTWARE	PHE A:135 , PHE A:136 , THR A:137 , ARG A:138 , HIS A:140 , CYS A:185 , ASP A:244 , TYR A:252 , HIS A:283 , ARG A:288 , GLY A:296 , ALA A:297 , SER A:299 , VAL A:300 , LYS A:301 , TRP A:302 , TYR A:322 , MO A:505	BINDING SITE FOR RESIDUE MTE A 501
06	AC6	SOFTWARE	CYS A:185 , MTE A:501 , HOH A:913 , HOH A:1329	BINDING SITE FOR RESIDUE MO A 505
07	AC7	SOFTWARE	VAL A:33 , PHE A:36 , HIS A:40 , PRO A:41 , GLY A:42 , LYS A:46 , ILE A:47 , ALA A:50 , PHE A:58 , TRP A:59 , HIS A:65 , HIS A:69 , HOH A:1030 , HOH A:1199	BINDING SITE FOR RESIDUE HEM A 502
08	AC8	SOFTWARE	PHE B:135 , PHE B:136 , THR B:137 , ARG B:138 , HIS B:140 , CYS B:185 , ASP B:244 , TYR B:252 , HIS B:283 , ARG B:288 , GLY B:296 , ALA B:297 , SER B:299 , VAL B:300 , LYS B:301 , TRP B:302 , TYR B:322 , MO B:505	BINDING SITE FOR RESIDUE MTE B 501
09	AC9	SOFTWARE	CYS B:185 , MTE B:501 , HOH B:912 , HOH B:1316	BINDING SITE FOR RESIDUE MO B 505
10	BC1	SOFTWARE	VAL B:33 , PHE B:36 , HIS B:40 , PRO B:41 , LYS B:46 , ILE B:47 , ALA B:50 , LEU B:55 , PHE B:58 , TRP B:59 , TYR B:62 , VAL B:64 , HIS B:65 , HIS B:69 , LEU B:74	BINDING SITE FOR RESIDUE HEM B 502
11	BC2	SOFTWARE	GLY B:161 , LEU B:163 , ARG B:173 , ARG B:197 , PRO B:198 , HIS B:225 , HOH B:1125 , HOH B:1213	BINDING SITE FOR RESIDUE EPE B 911
12	BC3	SOFTWARE	ARG A:337 , THR A:338 , ALA A:339 , PRO A:340 , HOH A:1259 , HOH B:1223	BINDING SITE FOR RESIDUE GOL A 912

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

Asymmetric/Biological Unit

No.	Residues
1	Lys A:113	-	Pro A:114
2	Phe A:285	-	Pro A:286
3	Gln A:353	-	Pro A:354
4	Lys B:113	-	Pro B:114
5	Phe B:285	-	Pro B:286
6	Gln B:353	-	Pro B:354

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_B5_2	PS50255	Cytochrome b5 family, heme-binding domain profile.	SUOX_CHICK	4-83	2	A:4-83 B:4-83
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	SUOX_CHICK	36-43	2	A:36-43 B:36-43
3	MOLYBDOPTERIN_EUK	PS00559	Eukaryotic molybdopterin oxidoreductases signature.	SUOX_CHICK	157-192	2	A:157-192 B:157-192

(no "Exon" information available for 1SOX)

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:463
 aligned with SUOX_CHICK | P07850 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  459       
                                    12        22        32        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       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452      |  -    
           SUOX_CHICK     3 SYPRYTREEVGRHRSPEERVWVTHGTDVFDVTDFVELHPGGPDKILLAAGGALEPFWALYAVHGEPHVLELLQQYKVGELSPDEAPAAPDAQDPFAGDPPRHPGLRVNSQKPFNAEPPAELLAERFLTPNELFFTRNHLPVPAVEPSSYRLRVDGPGGRTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGASLRDVLLHAGFPEELQGGEHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHRFPVRVVVPGVVGARSVKWLRRVAVSPDESPSRWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHR-------   -
               SCOP domains d1soxa2 A:3-93 Sulfite oxidase, N-terminal domain                                          d1soxa3 A:94-343 Sulfite oxidase, middle catalytic domain                                                                                                                                                                                                 d1soxa1 A:344-466 Sulfite oxidase, C-terminal domain                                                                        SCOP domains
               CATH domains 1soxA01 A:3-88 Flavocytochrome B2, subunit A, domain 1                                -1soxA02 A:90-343 Sulfite Oxidase; Chain A, domain 2                                                                                                                                                                                                           1soxA03 A:344-466  [code=2.60.40.650, no name defined]                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh........eeee..eeee...........hhhhhhh.....hhhhhh.hhhh.hhhhhhhhhheeee.......-..................eeee....eee..hhhh.......hhh.............hhh.eeeeee.....eeeehhhhhhh..eeeeeeeee.....hhhhh..............eeeeeeeeeehhhhhhhh..........eeeeee..........eeeeehhhhh......eeeeee.............eee.....hhh....eeeeeee......hhhh................hhh.........eeeeee.........eeeeeeeeee......eeeeeee.........................eeeeeeeee....eeeeeeeeee..........hhh...........eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CYTOCHROME_B5_2  PDB: A:4-83 UniProt: 4-83                                      -------------------------------------------------------------------------MOLYBDOPTERIN_EUK  PDB: A:157-192   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------CYTOCHRO--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sox A   3 SYPEYTREEVGRHRSPEERVWVTHGTDVFDVTDFVELHPGGPDKILLAAGGALEPFWALYAVHGEPHVLELLQQYKVGELSPDEAP-APDAQDPFAGDPPRHPGLRVNSQKPFNAEPPAELLAERFLTPNELFFTRNHLPVPAVEPSSYRLRVDGPGGGTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGARLRDVLLHAGFPEELQGEWHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHGFPVRVVVPGVVGARSVKWLRRVAVSPDESPSHWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHRVRVSVQD 466
                                    12        22        32        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       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462    
                                                                                                                88 |                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                                  90

Chain B from PDB  Type:PROTEIN  Length:458
 aligned with SUOX_CHICK | P07850 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  459       
                                    12        22        32        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       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452      |  -    
           SUOX_CHICK     3 SYPRYTREEVGRHRSPEERVWVTHGTDVFDVTDFVELHPGGPDKILLAAGGALEPFWALYAVHGEPHVLELLQQYKVGELSPDEAPAAPDAQDPFAGDPPRHPGLRVNSQKPFNAEPPAELLAERFLTPNELFFTRNHLPVPAVEPSSYRLRVDGPGGRTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGASLRDVLLHAGFPEELQGGEHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHRFPVRVVVPGVVGARSVKWLRRVAVSPDESPSRWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHR-------   -
               SCOP domains d1soxb2 B:3-93 Sulfite oxidase, N-terminal domain                                          d1soxb3 B:94-343 Sulfite oxidase, middle catalytic domain                                                                                                                                                                                                 d1soxb1 B:344-466 Sulfite oxidase, C-terminal domain                                                                        SCOP domains
               CATH domains 1soxB01 B:3-92 Flavocytochrome B2, subunit A, domain 1                                    1soxB02 B:93-343 Sulfite Oxidase; Chain A, domain 2                                                                                                                                                                                                        1soxB03 B:344-465  [code=2.60.40.650, no name defined]                                                                    - CATH domains
           Pfam domains (1) ---Cyt-b5-1soxB03 B:6-83                                                         ------------------------------------------------------Oxidored_molyb-1soxB05 B:138-319                                                                                                                                                      -------------------Mo-co_dimer-1soxB01 B:339-459                                                                                            ------- Pfam domains (1)
           Pfam domains (2) ---Cyt-b5-1soxB04 B:6-83                                                         ------------------------------------------------------Oxidored_molyb-1soxB06 B:138-319                                                                                                                                                      -------------------Mo-co_dimer-1soxB02 B:339-459                                                                                            ------- Pfam domains (2)
         Sec.struct. author ......hhhhhh........eeee..eeee....hhh....hhhhhhh.....hhhhhh.hhhh.hhhhhhhhhheeee....------................eeee....eee..hhh............................eeeeee.....eeeehhhhhh....eeeeeeee.....hhhhhhh............eeeeeeeeeehhhhhhh...........eeeeee..........eeeeehhhhh......eeeeee......hhh....eee.....hhh....eeeeeee......hhhh................hhh.........eeeeee.........eeeeeeeeee......eeeeeee.........................eeeeeeeee....eeeeeeeeee..........hhh...........eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CYTOCHROME_B5_2  PDB: B:4-83 UniProt: 4-83                                      -------------------------------------------------------------------------MOLYBDOPTERIN_EUK  PDB: B:157-192   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------CYTOCHRO--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sox B   3 SYPEYTREEVGRHRSPEERVWVTHGTDVFDVTDFVELHPGGPDKILLAAGGALEPFWALYAVHGEPHVLELLQQYKVGELSPD------DAQDPFAGDPPRHPGLRVNSQKPFNAEPPAELLAERFLTPNELFFTRNHLPVPAVEPSSYRLRVDGPGGGTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGARLRDVLLHAGFPEELQGEWHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHGFPVRVVVPGVVGARSVKWLRRVAVSPDESPSHWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHRVRVSVQD 466
                                    12        22        32        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       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462    
                                                                                                             85     92

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Sulfite Oxidase; Chain A, domain 2 (11)

Homologous Superfamily: Sulfite Oxidase; Chain A, domain 2 (11)

Chicken (Gallus gallus) (6)

1a	1soxA02	A:90-343
1b	1soxB02	B:93-343

Architecture: Roll (3276)

Topology: Flavocytochrome B2; Chain A, domain 1 (56)

Homologous Superfamily: Flavocytochrome B2, subunit A, domain 1 (56)

Chicken (Gallus gallus) (1)

2a	1soxA01	A:3-88
2b	1soxB01	B:3-92

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.650, no name defined] (9)

Chicken (Gallus gallus) (6)

3a	1soxA03	A:344-466
3b	1soxB03	B:344-465

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: E-set (290)

Family: Mo-co_dimer (3)

Gallus gallus (Chicken) (1)

1a	Mo-co_dimer-1soxB01	B:339-459
1b	Mo-co_dimer-1soxB02	B:339-459

Clan: no clan defined [family: Cyt-b5] (29)

Family: Cyt-b5 (29)

Gallus gallus (Chicken) (1)

2a	Cyt-b5-1soxB03	B:6-83
2b	Cyt-b5-1soxB04	B:6-83

Clan: no clan defined [family: Oxidored_molyb] (3)

Family: Oxidored_molyb (3)

Gallus gallus (Chicken) (1)

3a	Oxidored_molyb-1soxB05	B:138-319
3b	Oxidored_molyb-1soxB06	B:138-319

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SUOX_CHICK | P07850)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030151	molybdenum ion binding	Interacting selectively and non-covalently with molybdenum (Mo) ions.
	GO:0043546	molybdopterin cofactor binding	Interacting selectively and non-covalently with the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
	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:0008482	sulfite oxidase activity	Catalysis of the reaction: H(2)O + O(2) + sulfite = H(2)O(2) + H(+) + sulfate.
biological process
	GO:0042128	nitrate assimilation	The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
	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.
	GO:0006790	sulfur compound metabolic process	The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
cellular component
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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	SUOX_CHICK \| P07850	:	2a99 2a9a 2a9b 2a9c 2a9d 3hbg 3hbp 3hbq 3r18 3r19

(no "Related Entries Specified in the PDB File" available for 1SOX)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

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