1WNW - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 4 (Jmol Viewer)

Title :   D136N MUTANT OF HEME OXYGENASE FROM CORYNEBACTERIUM DIPHTHERIAE (HMUO)

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

Date :   10 Aug 04 (Deposition) - 09 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: B (1x),C (1x)

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

Reference :   T. Matsui, M. Furukawa, M. Unno, T. Tomita, M. Ikeda-Saito
Roles Of Distal Asp In Heme Oxygenase From Corynebacterium Diphtheriae, Hmuo: A Water-Driven Oxygen Activation Mechanism
J. Biol. Chem. V. 280 2981 2005
PubMed-ID: 15528205 | Reference-DOI: 10.1074/JBC.M410263200
(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 Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	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)	:		B (1x)	C (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 26)

No.	Name	Count	Type	Full Name
1	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	IOD	9	Ligand/Ion	IODIDE ION
3	NA	2	Ligand/Ion	SODIUM ION
4	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	IOD	4	Ligand/Ion	IODIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	IOD	4	Ligand/Ion	IODIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 6)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	IOD	1	Ligand/Ion	IODIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 10)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	IOD	4	Ligand/Ion	IODIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP C:96	BINDING SITE FOR RESIDUE IOD C 1001
02	AC2	SOFTWARE	MET B:29 , HEM B:902 , HOH B:4097	BINDING SITE FOR RESIDUE IOD B 1002
03	AC3	SOFTWARE	ASP B:154	BINDING SITE FOR RESIDUE IOD B 1003
04	AC4	SOFTWARE	IOD A:1007 , HOH A:2083 , HOH A:2132	BINDING SITE FOR RESIDUE IOD A 1006
05	AC5	SOFTWARE	HEM A:901 , IOD A:1006 , HOH A:2032	BINDING SITE FOR RESIDUE IOD A 1007
06	AC6	SOFTWARE	HOH A:2127	BINDING SITE FOR RESIDUE IOD A 1008
07	AC7	SOFTWARE	ASP B:108 , GLN B:206	BINDING SITE FOR RESIDUE NA B 4001
08	AC8	SOFTWARE	HOH B:4062 , HOH B:4157	BINDING SITE FOR RESIDUE NA B 4002
09	AC9	SOFTWARE	VAL C:82 , ARG C:85 , GLY C:159 , HOH C:2091	BINDING SITE FOR RESIDUE SO4 C 2001
10	BC1	SOFTWARE	TYR C:161 , HIS C:162 , PHE C:163 , LEU C:169	BINDING SITE FOR RESIDUE SO4 C 2002
11	BC2	SOFTWARE	SER B:26 , THR B:27 , HIS B:205 , HOH B:4105	BINDING SITE FOR RESIDUE SO4 B 2003
12	BC3	SOFTWARE	VAL B:82 , ARG B:85 , GLY B:159 , HOH B:4017	BINDING SITE FOR RESIDUE SO4 B 2004
13	BC4	SOFTWARE	LYS B:170 , LYS B:173 , ARG B:177 , HOH B:4078	BINDING SITE FOR RESIDUE SO4 B 2005
14	BC5	SOFTWARE	VAL A:202 , GLY B:165 , ILE B:166 , ALA B:167	BINDING SITE FOR RESIDUE SO4 B 2006
15	BC6	SOFTWARE	PRO A:123 , GLU A:188 , GLN A:189 , HIS A:192 , HOH A:2104	BINDING SITE FOR RESIDUE SO4 A 2007
16	BC7	SOFTWARE	ARG B:44 , ARG B:99 , HOH B:4111	BINDING SITE FOR RESIDUE SO4 B 2008
17	BC8	SOFTWARE	ARG A:97 , HOH A:2016 , HOH A:2137	BINDING SITE FOR RESIDUE SO4 A 2009
18	BC9	SOFTWARE	LYS C:89 , LEU C:90 , GLY C:152 , VAL C:153 , ASP C:154 , ALA C:157	BINDING SITE FOR RESIDUE SO4 C 2010
19	CC1	SOFTWARE	LYS A:13 , LYS A:173 , ARG A:177 , HOH A:2077	BINDING SITE FOR RESIDUE SO4 A 2011
20	CC2	SOFTWARE	HOH B:4035 , HOH B:4053 , HOH C:2059	BINDING SITE FOR RESIDUE SO4 C 2012
21	CC3	SOFTWARE	LYS A:13 , HIS A:20 , ALA A:23 , GLU A:24 , LEU A:33 , TYR A:130 , VAL A:131 , GLY A:135 , SER A:138 , GLY A:139 , ARG A:177 , ASN A:204 , PHE A:208 , IOD A:1007 , HOH A:2033 , HOH A:2126 , HOH A:2138	BINDING SITE FOR RESIDUE HEM A 901
22	CC4	SOFTWARE	LYS B:13 , HIS B:20 , ALA B:23 , LEU B:33 , TYR B:130 , VAL B:131 , GLY B:135 , SER B:138 , ARG B:177 , PHE B:201 , ASN B:204 , PHE B:208 , IOD B:1002 , HOH B:4010 , HOH B:4078 , HOH B:4159	BINDING SITE FOR RESIDUE HEM B 902
23	CC5	SOFTWARE	LYS C:13 , HIS C:20 , ALA C:23 , LEU C:33 , TYR C:130 , VAL C:131 , GLY C:135 , SER C:138 , ARG C:177 , PHE C:201 , ASN C:204 , HOH C:2062 , HOH C:2085	BINDING SITE FOR RESIDUE HEM C 903

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

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

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

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:125-135 C:125-135

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:125-135 -

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:125-135

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	- B:125-135 C:125-135

(no "Exon" information available for 1WNW)

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: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 d1wnwa_ A: Heme oxygenase HmuO                                                                                                                                                                                   SCOP domains
               CATH domains 1wnwA00 A:6-213 Heme Oxygenase; Chain A                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wnw A   6 AGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGNLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 213
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with HMUO_CORDI | P71119 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:210
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215
           HMUO_CORDI     6 AGLAVELKQSTAQAHEKAEHSTFMSDLLEGRLGVAEFTRLQEQAWLFYTALEQAADAVRASGFAESLLDPALNRAEVLARDLDKLNDGSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQRENLLKEATDAFVFNHQVFADLGKGL 215
               SCOP domains d1wnwb_ B: Heme oxygenase HmuO                                                                                                                                                                                     SCOP domains
               CATH domains 1wnwB00 B:6-215 Heme Oxygenase; Chain A                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN-------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wnw B   6 AGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGNLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL 215
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215

Chain C from PDB  Type:PROTEIN  Length:206
 aligned with HMUO_CORDI | P71119 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:206
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206      
           HMUO_CORDI     7 GLAVELKQSTAQAHEKAEHSTFMSDLLEGRLGVAEFTRLQEQAWLFYTALEQAADAVRASGFAESLLDPALNRAEVLARDLDKLNDGSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQRENLLKEATDAFVFNHQVFADLG 212
               SCOP domains d1wnwc_ C: Heme oxygenase HmuO                                                                                                                                                                                 SCOP domains
               CATH domains 1wnwC00 C:7-212 Heme Oxygenase; Chain A                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN----------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wnw C   7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGNLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLG 212
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206

Legend:		→ Mismatch	(orange background)
	-	→ 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( (-)

)

Families(

)

Protein Domains( (-)

)

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	d1wnwa_	A:
1b	d1wnwb_	B:
1c	d1wnwc_	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	1wnwB00	B:6-215
1b	1wnwA00	A:6-213
1c	1wnwC00	C:7-212

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

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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	1wnw
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	1.14.99.3
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UniProtKB/Swiss-Prot
	HMUO_CORDI \| P71119	:	1iw0 1iw1 1v8x 1wnv 1wnx 1wzd 1wzf 1wzg

1iw0	FERRIC WILD TYPE
1iw1	FERROUS WILD TYPE
1v8x	THE SAME PROTEIN COMPLEX WITH DIOXYGEN
1wnv	ANOTHER VARIANT OF THE SAME PROTEIN
1wnx	D136E MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 26)

Sites (23, 23)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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