1V8X - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DIOXYGEN-BOUND HEME OXYGENASE FROM CORYNEBACTERIUM DIPHTHERIAE

Authors :   M. Unno, T. Matsui, G. C. Chu, M. Couture, T. Yoshida, D. L. Rousseau, J. S. Olson, M. Ikeda-Saito

Date :   15 Jan 04 (Deposition) - 18 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Protein-Heme Complex, Helix, Oxy, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Unno, T. Matsui, G. C. Chu, M. Couture, T. Yoshida, D. L. Rousseau, J. S. Olson, M. Ikeda-Saito
Crystal Structure Of The Dioxygen-Bound Heme Oxygenase From Corynebacterium Diphtheriae: Implications For Heme Oxygenase Function.
J. Biol. Chem. V. 279 21055 2004
PubMed-ID: 14966119 | Reference-DOI: 10.1074/JBC.M400491200
(for further references see the PDB file header)

Molecule 1 - HEME OXYGENASE
	Chains	:	A, B, C
	EC Number	:	1.14.99.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMW172
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	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 (4, 19)

No.	Name	Count	Type	Full Name
1	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	OXY	3	Ligand/Ion	OXYGEN MOLECULE
3	SO4	12	Ligand/Ion	SULFATE ION
4	SUC	1	Ligand/Ion	SUCROSE

Biological Unit 1 (4, 6)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	OXY	1	Ligand/Ion	OXYGEN MOLECULE
3	SO4	3	Ligand/Ion	SULFATE ION
4	SUC	1	Ligand/Ion	SUCROSE

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	OXY	1	Ligand/Ion	OXYGEN MOLECULE
3	SO4	4	Ligand/Ion	SULFATE ION
4	SUC	-1	Ligand/Ion	SUCROSE

Biological Unit 3 (3, 7)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	OXY	1	Ligand/Ion	OXYGEN MOLECULE
3	SO4	5	Ligand/Ion	SULFATE ION
4	SUC	-1	Ligand/Ion	SUCROSE

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:13 , ALA A:17 , HIS A:20 , GLU A:21 , HEM A:901 , HOH A:5008 , HOH A:5019 , HOH A:5067 , HOH A:5113	BINDING SITE FOR RESIDUE SUC A 3001
02	AC2	SOFTWARE	LYS A:173 , ARG A:177 , HEM A:901 , HOH A:5011 , HOH A:5149	BINDING SITE FOR RESIDUE SO4 A 2003
03	AC3	SOFTWARE	SER A:26 , THR A:27 , HIS A:205 , HOH A:5073	BINDING SITE FOR RESIDUE SO4 A 2007
04	AC4	SOFTWARE	LYS A:168 , LEU A:169 , LYS A:170 , HOH A:5089 , HOH A:5145	BINDING SITE FOR RESIDUE SO4 A 2011
05	AC5	SOFTWARE	LYS A:13 , HIS A:20 , MET A:29 , LEU A:33 , TYR A:130 , VAL A:131 , GLY A:135 , SER A:138 , GLY A:139 , LYS A:173 , ARG A:177 , PHE A:201 , PHE A:208 , SO4 A:2003 , SUC A:3001 , OXY A:5001 , HOH A:5011 , HOH A:5047 , HOH A:5108	BINDING SITE FOR RESIDUE HEM A 901
06	AC6	SOFTWARE	GLY A:135 , GLY A:139 , GLY A:140 , HEM A:901 , HOH A:5064	BINDING SITE FOR RESIDUE OXY A 5001
07	AC7	SOFTWARE	LYS B:470 , LYS B:473 , ARG B:477 , HOH B:5091	BINDING SITE FOR RESIDUE SO4 B 2001
08	AC8	SOFTWARE	GLY B:367 , ALA B:369 , GLU B:370 , SER B:371 , HOH B:5064 , HOH B:5111 , HOH B:5134 , HOH B:5135	BINDING SITE FOR RESIDUE SO4 B 2006
09	AC9	SOFTWARE	THR B:327 , HIS B:505 , HOH B:5098	BINDING SITE FOR RESIDUE SO4 B 2008
10	BC1	SOFTWARE	VAL B:382 , ARG B:385 , GLY B:459 , HOH B:5018	BINDING SITE FOR RESIDUE SO4 B 2009
11	BC2	SOFTWARE	LYS B:313 , HIS B:320 , ALA B:323 , GLU B:324 , 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 , OXY B:5002 , HOH B:5015	BINDING SITE FOR RESIDUE HEM B 902
12	BC3	SOFTWARE	GLY B:435 , GLY B:439 , GLY B:440 , HEM B:902 , HOH B:5083	BINDING SITE FOR RESIDUE OXY B 5002
13	BC4	SOFTWARE	HOH C:138 , HOH C:143 , ARG C:685 , GLY C:759	BINDING SITE FOR RESIDUE SO4 C 2002
14	BC5	SOFTWARE	HOH C:232 , HOH C:323 , GLY C:638 , VAL C:639 , ALA C:640	BINDING SITE FOR RESIDUE SO4 C 2004
15	BC6	SOFTWARE	HOH C:142 , HOH C:265 , GLY C:667 , ALA C:669 , GLU C:670 , SER C:671	BINDING SITE FOR RESIDUE SO4 C 2005
16	BC7	SOFTWARE	ARG C:745 , ARG C:749	BINDING SITE FOR RESIDUE SO4 C 2010
17	BC8	SOFTWARE	SER C:626 , THR C:627 , PHE C:628	BINDING SITE FOR RESIDUE SO4 C 2012
18	BC9	SOFTWARE	HOH C:141 , HOH C:194 , HOH C:360 , LYS C:613 , HIS C:620 , ALA C:623 , GLU C:624 , TYR C:730 , VAL C:731 , GLY C:735 , SER C:738 , ARG C:777 , PHE C:801 , ASN C:804 , PHE C:808 , OXY C:5003	BINDING SITE FOR RESIDUE HEM C 903
19	CC1	SOFTWARE	HOH C:218 , GLY C:735 , GLY C:739 , HEM C:903	BINDING SITE FOR RESIDUE OXY C 5003

(no "SS Bond" information available for 1V8X)

(no "Cis Peptide Bond" information available for 1V8X)

(no "SAP(SNP)/Variant" information available for 1V8X)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEME_OXYGENASE	PS00593	Heme oxygenase signature.	HMUO_CORDI	125-135	3	A:125-135 B:425-435 C:725-735

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEME_OXYGENASE	PS00593	Heme oxygenase signature.	HMUO_CORDI	125-135	1	A:125-135 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEME_OXYGENASE	PS00593	Heme oxygenase signature.	HMUO_CORDI	125-135	1	- B:425-435 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEME_OXYGENASE	PS00593	Heme oxygenase signature.	HMUO_CORDI	125-135	1	- - C:725-735

(no "Exon" information available for 1V8X)

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:210
 aligned with HMUO_CORDI | P71119 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:210
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214
           HMUO_CORDI     5 TAGLAVELKQSTAQAHEKAEHSTFMSDLLEGRLGVAEFTRLQEQAWLFYTALEQAADAVRASGFAESLLDPALNRAEVLARDLDKLNDGSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQRENLLKEATDAFVFNHQVFADLGKG 214
               SCOP domains d1v8xa_ A: Heme oxygenase HmuO                                                                                                                                                                                     SCOP domains
               CATH domains 1v8xA00 A:5-214 Heme Oxygenase; Chain A                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------HEME_OXYGEN------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v8x A   5 TAGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKG 214
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with HMUO_CORDI | P71119 from UniProtKB/Swiss-Prot  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         
           HMUO_CORDI     7 GLAVELKQSTAQAHEKAEHSTFMSDLLEGRLGVAEFTRLQEQAWLFYTALEQAADAVRASGFAESLLDPALNRAEVLARDLDKLNDGSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQRENLLKEATDAFVFNHQVFADLGKGL 215
               SCOP domains d1v8xb_ B: Heme oxygenase HmuO                                                                                                                                                                                    SCOP domains
               CATH domains 1v8xB00 B:307-515 Heme Oxygenase; Chain A                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN-------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v8x 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:208
 aligned with HMUO_CORDI | P71119 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:208
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
           HMUO_CORDI     6 AGLAVELKQSTAQAHEKAEHSTFMSDLLEGRLGVAEFTRLQEQAWLFYTALEQAADAVRASGFAESLLDPALNRAEVLARDLDKLNDGSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQRENLLKEATDAFVFNHQVFADLGK 213
               SCOP domains d1v8xc_ C: Heme oxygenase HmuO                                                                                                                                                                                   SCOP domains
               CATH domains 1v8xC00 C:606-813 Heme Oxygenase; Chain A                                                                                                                                                                        CATH domains
           Pfam domains (1) Heme_oxygenase-1v8xC01 C:606-810                                                                                                                                                                             --- Pfam domains (1)
           Pfam domains (2) Heme_oxygenase-1v8xC02 C:606-810                                                                                                                                                                             --- Pfam domains (2)
           Pfam domains (3) Heme_oxygenase-1v8xC03 C:606-810                                                                                                                                                                             --- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v8x C 606 AGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 813
                                   615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805

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	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	d1v8xa_	A:
1b	d1v8xb_	B:
1c	d1v8xc_	C:

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	1v8xA00	A:5-214
1b	1v8xB00	B:307-515
1c	1v8xC00	C:606-813

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HO (49)

Family: Heme_oxygenase (37)

Corynebacterium diphtheriae (6)

1a	Heme_oxygenase-1v8xC01	C:606-810
1b	Heme_oxygenase-1v8xC02	C:606-810
1c	Heme_oxygenase-1v8xC03	C:606-810

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (HMUO_CORDI | P71119)

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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	Cis Peptide Bonds
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	1v8x
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	HMUO_CORDI \| P71119	:	1iw0 1iw1 1wnv 1wnw 1wnx 1wzd 1wzf 1wzg

1iw0	THE SAME PROTEIN (FERRIC FORM)
1iw1	THE SAME PROTEIN (FERROUS FORM)

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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