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Title :   CRYSTAL STRUCTURE OF A HEME OXYGENASE (HMUO) FROM CORYNEBACTERIUM DIPHTHERIAE COMPLEXED WITH HEME IN THE FERROUS STATE

Authors :   S. Hirotsu, M. Unno, G. C. Chu, D. S. Lee, S. Y. Park, Y. Shiro, M. Ikeda- Saito, Riken Structural Genomics/Proteomics Initiative (Rsgi

Date :   04 Apr 02 (Deposition) - 04 Apr 03 (Release) - 24 Feb 09 (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)
Biol. Unit 4: A (1x),B (1x)

Keywords :   Alpha Helix, Bacterial Iron Acquisition, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Hirotsu, G. C. Chu, M. Unno, D. S. Lee, T. Yoshida, S. Y. Park, Y. Shiro, M. Ikeda-Saito
The Crystal Structures Of The Ferric And Ferrous Forms Of The Heme Complex Of Hmuo, A Heme Oxygenase Of Corynebacterium Diphtheriae.
J. Biol. Chem. V. 279 11937 2004
PubMed-ID: 14645223 | Reference-DOI: 10.1074/JBC.M311631200
(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 BL21(DE3)
	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
Biological Unit 4 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	10	Ligand/Ion	SULFATE ION
3	SUC	1	Ligand/Ion	SUCROSE

Biological Unit 1 (3, 7)

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

Biological Unit 2 (2, 6)

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

Biological Unit 3 (1, 1)

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

Biological Unit 4 (3, 7)

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

Asymmetric Unit (14, 14)

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:1004 , HOH A:1111 , HOH A:1126 , HOH A:1179	BINDING SITE FOR RESIDUE SUC A 904
02	AC2	SOFTWARE	ARG A:99 , ILE A:100 , THR A:101 , HOH A:1033 , HOH A:1062 , HOH A:1219	BINDING SITE FOR RESIDUE SO4 A 905
03	AC3	SOFTWARE	GLY B:367 , ALA B:369 , GLU B:370 , SER B:371 , HOH B:2020 , HOH B:2050 , HOH B:2060 , HOH B:2129	BINDING SITE FOR RESIDUE SO4 B 906
04	AC4	SOFTWARE	GLN A:58 , HOH A:1106	BINDING SITE FOR RESIDUE SO4 A 907
05	AC5	SOFTWARE	GLY A:67 , ALA A:69 , GLU A:70 , SER A:71 , HOH A:1021 , HOH A:1051 , HOH A:1142 , HOH A:1146 , HOH A:1237	BINDING SITE FOR RESIDUE SO4 A 908
06	AC6	SOFTWARE	TYR A:151 , GLY A:152 , HOH A:1208	BINDING SITE FOR RESIDUE SO4 A 909
07	AC7	SOFTWARE	SER B:326 , THR B:327 , HIS B:505 , HOH B:2122 , HOH B:2143 , HOH B:2174	BINDING SITE FOR RESIDUE SO4 B 910
08	AC8	SOFTWARE	HOH A:1173 , ARG B:445 , ARG B:449 , HOH B:2131	BINDING SITE FOR RESIDUE SO4 B 911
09	AC9	SOFTWARE	ARG B:344	BINDING SITE FOR RESIDUE SO4 B 912
10	BC1	SOFTWARE	LYS B:470 , LYS B:473 , ARG B:477 , HOH B:2091	BINDING SITE FOR RESIDUE SO4 B 913
11	BC2	SOFTWARE	ILE A:107 , ASN A:111 , HOH A:1082 , HOH A:1173 , HOH A:1239 , HOH A:1240 , HOH B:2089	BINDING SITE FOR RESIDUE SO4 A 914
12	BC3	SOFTWARE	LYS A:13 , HIS A:20 , GLU A:24 , MET A:29 , TYR A:130 , VAL A:131 , ARG A:132 , GLY A:135 , SER A:138 , GLY A:139 , VAL A:142 , LYS A:173 , ARG A:177 , PHE A:201 , PHE A:208 , SUC A:904 , HOH A:1040 , HOH A:1189 , HOH A:1190 , HOH A:1220	BINDING SITE FOR RESIDUE HEM A 901
13	BC4	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 , HOH B:2039	BINDING SITE FOR RESIDUE HEM B 902
14	BC5	SOFTWARE	LYS C:613 , HIS C:620 , ALA C:623 , GLU C:624 , TYR C:730 , VAL C:731 , GLY C:735 , SER C:738 , VAL C:742 , ARG C:777 , PHE C:801 , PHE C:808 , HOH C:2057	BINDING SITE FOR RESIDUE HEM C 903

(no "SS Bond" information available for 1IW1)

(no "Cis Peptide Bond" information available for 1IW1)

(no "SAP(SNP)/Variant" information available for 1IW1)

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

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEME_OXYGENASE	PS00593	Heme oxygenase signature.	HMUO_CORDI	125-135	2	A:125-135 B:425-435 -

(no "Exon" information available for 1IW1)

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:212
 aligned with HMUO_CORDI | P71119 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
           HMUO_CORDI     2 TTATAGLAVELKQSTAQAHEKAEHSTFMSDLLEGRLGVAEFTRLQEQAWLFYTALEQAADAVRASGFAESLLDPALNRAEVLARDLDKLNDGSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQRENLLKEATDAFVFNHQVFADLGK 213
               SCOP domains d1iw1a_ A: Heme oxygenase HmuO                                                                                                                                                                                       SCOP domains
               CATH domains 1iw1A00 A:2-213 Heme Oxygenase; Chain A                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------HEME_OXYGEN------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iw1 A   2 TTATAGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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 d1iw1b_ B: Heme oxygenase HmuO                                                                                                                                                                                    SCOP domains
               CATH domains 1iw1B00 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 ----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN-------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iw1 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 d1iw1c_ C: Heme oxygenase HmuO                                                                                                                                                                                   SCOP domains
               CATH domains 1iw1C00 C:606-813 Heme Oxygenase; Chain A                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iw1 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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	-	→ Gap	(green background, '-', border residues have a numbering label)
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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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

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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	d1iw1a_	A:
1b	d1iw1b_	B:
1c	d1iw1c_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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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	1iw1A00	A:2-213
1b	1iw1B00	B:307-515
1c	1iw1C00	C:606-813

(no "Pfam Domain" information available for 1IW1)

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.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1iw1)

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	HMUO_CORDI \| P71119	:	1iw0 1v8x 1wnv 1wnw 1wnx 1wzd 1wzf 1wzg

1iw0	1IW0 CONTAINS THE SAME PROTEIN COMPLEXED WITH HEME IN FERRIC STATE RELATED ID: MY_001000032.2 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

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