1WNV - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   D136A MUTANT OF HEME OXYGENASE FROM CORYNEBACTERIUM DIPHTHERIAE (HMUO)

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

Date :   10 Aug 04 (Deposition) - 09 Nov 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)
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 BL21(DE3)
	Expression System Plasmid	:	PMW172
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	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 (2, 8)

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

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 3)

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

Biological Unit 3 (2, 3)

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

Biological Unit 4 (2, 3)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:40 , LYS B:470 , LYS B:473 , ARG B:477	BINDING SITE FOR RESIDUE SO4 B 2011
2	AC2	SOFTWARE	VAL B:382 , ARG B:385 , GLY B:459 , HOH B:1040 , HOH B:1216	BINDING SITE FOR RESIDUE SO4 B 2012
3	AC3	SOFTWARE	SER A:26 , THR A:27 , HIS A:205 , HOH A:2067	BINDING SITE FOR RESIDUE SO4 A 2013
4	AC4	SOFTWARE	ARG C:745 , ARG C:749	BINDING SITE FOR RESIDUE SO4 C 2014
5	AC5	SOFTWARE	VAL C:682 , ARG C:685 , GLY C:759 , GLU C:764 , HOH C:1103 , HOH C:1155	BINDING SITE FOR RESIDUE SO4 C 2015
6	AC6	SOFTWARE	LYS A:13 , HIS A:20 , ALA A:23 , TYR A:130 , VAL A:131 , GLY A:135 , SER A:138 , ARG A:177 , PHE A:201 , ASN A:204 , PHE A:208 , HOH A:2062 , HOH A:2070 , HOH A:2072 , HOH A:2075 , HOH A:2078	BINDING SITE FOR RESIDUE HEM A 901
7	AC7	SOFTWARE	HOH B:114 , 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 , VAL B:442 , ARG B:477 , PHE B:501 , ASN B:504 , PHE B:508 , HOH B:1035	BINDING SITE FOR RESIDUE HEM B 902
8	AC8	SOFTWARE	HOH C:8 , HOH C:93 , LYS C:613 , HIS C:620 , ALA C:623 , GLU C:624 , LEU C:633 , TYR C:730 , VAL C:731 , GLY C:735 , SER C:738 , ARG C:777 , ASN C:804 , HOH C:1039	BINDING SITE FOR RESIDUE HEM C 903

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

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

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

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	- B:425-435 C:725-735

(no "Exon" information available for 1WNV)

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 HMUO_CORDI | P71119 from UniProtKB/Swiss-Prot  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       
           HMUO_CORDI     7 GLAVELKQSTAQAHEKAEHSTFMSDLLEGRLGVAEFTRLQEQAWLFYTALEQAADAVRASGFAESLLDPALNRAEVLARDLDKLNDGSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQRENLLKEATDAFVFNHQVFADLGK 213
               SCOP domains d1wnva_ A: Heme oxygenase HmuO                                                                                                                                                                                  SCOP domains
               CATH domains 1wnvA00 A:7-213 Heme Oxygenase; Chain A                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wnv A   7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGALSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 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: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 d1wnvb_ B: Heme oxygenase HmuO                                                                                                                                                                                     SCOP domains
               CATH domains 1wnvB00 B:306-515 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
                 1wnv B 306 AGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGALSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL 515
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515

Chain C from PDB  Type:PROTEIN  Length:207
 aligned with HMUO_CORDI | P71119 from UniProtKB/Swiss-Prot  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       
           HMUO_CORDI     7 GLAVELKQSTAQAHEKAEHSTFMSDLLEGRLGVAEFTRLQEQAWLFYTALEQAADAVRASGFAESLLDPALNRAEVLARDLDKLNDGSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQRENLLKEATDAFVFNHQVFADLGK 213
               SCOP domains d1wnvc_ C: Heme oxygenase HmuO                                                                                                                                                                                  SCOP domains
               CATH domains 1wnvC00 C:607-813 Heme Oxygenase; Chain A                                                                                                                                                                       CATH domains
           Pfam domains (1) Heme_oxygenase-1wnvC01 C:607-810                                                                                                                                                                            --- Pfam domains (1)
           Pfam domains (2) Heme_oxygenase-1wnvC02 C:607-810                                                                                                                                                                            --- Pfam domains (2)
           Pfam domains (3) Heme_oxygenase-1wnvC03 C:607-810                                                                                                                                                                            --- Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wnv C 607 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGALSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 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(

)

Folds(

)

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	d1wnva_	A:
1b	d1wnvb_	B:
1c	d1wnvc_	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	1wnvB00	B:306-515
1b	1wnvA00	A:7-213
1c	1wnvC00	C:607-813

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HO (49)

Family: Heme_oxygenase (37)

Corynebacterium diphtheriae (6)

1a	Heme_oxygenase-1wnvC01	C:607-810
1b	Heme_oxygenase-1wnvC02	C:607-810
1c	Heme_oxygenase-1wnvC03	C:607-810

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

1iw0	FERRIC WILD TYPE
1iw1	FERROUS WILD TYPE
1v8x	THE SAME PROTEIN COMPLEX WITH DIOXYGEN
1wnw	D136N MUTANT
1wnx	D136E MUTANT

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