3I8R - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE HEME OXYGENASE FROM CORYNEBACTERIUM DIPHTHERIAE (HMUO) IN COMPLEX WITH HEME BINDING DITIOTHREITOL (DTT)

Authors :   T. Matsui, M. Unno, M. Ikeda-Saito

Date :   10 Jul 09 (Deposition) - 19 May 10 (Release) - 19 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Inhibitor, Heme Oxygenase, Dtt, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Matsui, M. Iwasaki, R. Sugiyama, M. Unno, M. Ikeda-Saito
Dioxygen Activation For The Self-Degradation Of Heme: Reaction Mechanism And Regulation Of Heme Oxygenase.
Inorg. Chem. V. 49 3602 2010
PubMed-ID: 20380462 | Reference-DOI: 10.1021/IC901869T

Molecule 1 - HEME OXYGENASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMW
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	CORYNEBACTERIUM DIPHTHERIAE
	Organism Taxid	:	1717

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	DTV	3	Ligand/Ion	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
2	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	DTV	1	Ligand/Ion	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	DTV	1	Ligand/Ion	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 5)

No.	Name	Count	Type	Full Name
1	DTV	1	Ligand/Ion	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:13 , HIS A:20 , ALA A:23 , MET A:29 , TYR A:130 , VAL A:131 , GLY A:135 , VAL A:142 , ARG A:177 , PHE A:201 , ASN A:204 , PHE A:208 , HOH A:235 , HOH A:361 , HOH A:419 , DTV A:2001	BINDING SITE FOR RESIDUE HEM A 901
02	AC2	SOFTWARE	SER A:26 , THR A:27 , HIS A:205 , HOH A:279 , HOH A:286	BINDING SITE FOR RESIDUE SO4 A 1001
03	AC3	SOFTWARE	ARG A:99 , ILE A:100 , THR A:101	BINDING SITE FOR RESIDUE SO4 A 1005
04	AC4	SOFTWARE	ARG A:132 , GLY A:135 , ASP A:136 , GLY A:139 , GLY A:140 , HOH A:326 , HEM A:901	BINDING SITE FOR RESIDUE DTV A 2001
05	AC5	SOFTWARE	HOH B:25 , HOH B:185 , LYS B:313 , HIS B:320 , ALA B:323 , MET B:329 , LEU B:333 , TYR B:430 , VAL B:431 , GLY B:435 , SER B:438 , GLY B:439 , ARG B:477 , PHE B:501 , ASN B:504 , PHE B:508 , DTV B:2002	BINDING SITE FOR RESIDUE HEM B 902
06	AC6	SOFTWARE	HOH B:18 , VAL B:382 , ARG B:385 , GLY B:459 , HOH B:532	BINDING SITE FOR RESIDUE SO4 B 1002
07	AC7	SOFTWARE	HOH B:67 , HOH B:289 , LYS B:470 , LYS B:473 , ARG B:477	BINDING SITE FOR RESIDUE SO4 B 1003
08	AC8	SOFTWARE	HOH B:196 , SER B:326 , THR B:327 , HIS B:505 , ALA B:509	BINDING SITE FOR RESIDUE SO4 B 1004
09	AC9	SOFTWARE	HOH B:61 , HOH B:213 , GLY B:367 , ALA B:369 , GLU B:370 , SER B:371 , HOH B:516	BINDING SITE FOR RESIDUE SO4 B 1008
10	BC1	SOFTWARE	HOH B:3 , HOH B:5 , HOH B:130 , MET B:329 , ARG B:432 , GLY B:435 , GLY B:439 , ILE B:443 , PHE B:508 , HEM B:902	BINDING SITE FOR RESIDUE DTV B 2002
11	BC2	SOFTWARE	HOH C:158 , HOH C:226 , LYS C:613 , HIS C:620 , ALA C:623 , GLU C:624 , TYR C:730 , VAL C:731 , LEU C:734 , GLY C:735 , SER C:738 , GLY C:739 , VAL C:742 , ILE C:743 , ARG C:777 , PHE C:801 , ASN C:804 , PHE C:808 , DTV C:2003	BINDING SITE FOR RESIDUE HEM C 903
12	BC3	SOFTWARE	SER C:626 , THR C:627 , PHE C:628 , HIS C:805 , ALA C:809	BINDING SITE FOR RESIDUE SO4 C 1009
13	BC4	SOFTWARE	HOH C:212 , HOH C:356 , GLY C:667 , ALA C:669 , GLU C:670 , SER C:671	BINDING SITE FOR RESIDUE SO4 C 1010
14	BC5	SOFTWARE	HOH C:403 , VAL C:682 , ARG C:685 , GLY C:759	BINDING SITE FOR RESIDUE SO4 C 1011
15	BC6	SOFTWARE	HOH C:118 , HOH C:202 , HOH C:346 , MET C:629 , ARG C:732 , GLY C:735 , ASP C:736 , GLY C:739 , PHE C:808 , HEM C:903	BINDING SITE FOR RESIDUE DTV C 2003

(no "SS Bond" information available for 3I8R)

(no "Cis Peptide Bond" information available for 3I8R)

(no "SAP(SNP)/Variant" information available for 3I8R)

(no "PROSITE Motif" information available for 3I8R)

(no "Exon" information available for 3I8R)

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:207
 aligned with Q54AI1_CORDP | Q54AI1 from UniProtKB/TrEMBL  Length:215

    Alignment length:207
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       
         Q54AI1_CORDP     7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 213
               SCOP domains d3i8ra_ A: Heme oxygenase HmuO                                                                                                                                                                                  SCOP domains
               CATH domains 3i8rA00 A:7-213 Heme Oxygenase; Chain A                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i8r A   7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 213
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with Q54AI1_CORDP | Q54AI1 from UniProtKB/TrEMBL  Length:215

    Alignment length:209
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206         
         Q54AI1_CORDP     7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL 215
               SCOP domains d3i8rb_ B: Heme oxygenase HmuO                                                                                                                                                                                    SCOP domains
               CATH domains 3i8rB00 B:307-515 Heme Oxygenase; Chain A                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i8r B 307 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL 515
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506

Chain C from PDB  Type:PROTEIN  Length:207
 aligned with Q54AI1_CORDP | Q54AI1 from UniProtKB/TrEMBL  Length:215

    Alignment length:207
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       
         Q54AI1_CORDP     7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 213
               SCOP domains d3i8rc_ C: Heme oxygenase HmuO                                                                                                                                                                                  SCOP domains
               CATH domains 3i8rC00 C:607-813 Heme Oxygenase; Chain A                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i8r C 607 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 813
                                   616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Heme oxygenase-like (107)

Superfamily: Heme oxygenase-like (107)

Family: Eukaryotic type heme oxygenase (69)

Protein domain: Heme oxygenase HmuO (16)

Corynebacterium diphtheriae [TaxId: 1717] (16)

1a	d3i8ra_	A:
1b	d3i8rc_	C:
1c	d3i8rb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Heme Oxygenase; Chain A (84)

Homologous Superfamily: Heme Oxygenase; Chain A (84)

Corynebacterium diphtheriae. Organism_taxid: 1717. (11)

1a	3i8rB00	B:307-515
1b	3i8rC00	C:607-813
1c	3i8rA00	A:7-213

(no "Pfam Domain" information available for 3I8R)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q54AI1_CORDP | Q54AI1)

molecular function
	GO:0004392	heme oxygenase (decyclizing) activity	Catalysis of the reaction: heme + 3 donor-H2 + 3 O2 = biliverdin + Fe2+ + CO + 3 acceptor + 3 H2O.
	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.
biological process
	GO:0006788	heme oxidation	The chemical reactions and pathways resulting in the loss of electrons from one or more atoms in heme.
	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.

Asymmetric Unit
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