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(-) Description

Title :  D136E 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 :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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)

(-) Compounds

Molecule 1 - HEME OXYGENASE
    Chains: A, B
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA1Ligand/IonSODIUM ION
3SO411Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA-1Ligand/IonSODIUM ION
3SO45Ligand/IonSULFATE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA-1Ligand/IonSODIUM ION
3SO46Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:26 , THR A:27 , HOH A:3047BINDING SITE FOR RESIDUE SO4 A 1001
02AC2SOFTWAREARG B:112 , HIS B:192 , HOH B:1079BINDING SITE FOR RESIDUE SO4 B 1002
03AC3SOFTWAREGLN A:14 , GLU A:81 , ALA A:84 , ARG A:97 , HOH A:3027 , HOH A:3115 , HOH A:3124 , HOH B:1099BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWAREGLN A:58 , LYS A:173 , ARG A:177 , HEM A:901 , HOH A:3138BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWAREALA A:69 , GLU A:70 , SER A:71 , HOH A:3048 , HOH A:3058 , HOH A:3068 , LYS B:168BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWARELEU A:169 , LYS A:170BINDING SITE FOR RESIDUE SO4 A 1006
07AC7SOFTWARETHR A:101 , SER A:103 , THR B:27 , HOH B:1072 , HOH B:1143BINDING SITE FOR RESIDUE SO4 B 1007
08AC8SOFTWAREPRO B:75 , ALA B:76 , ASN B:78 , HOH B:1159BINDING SITE FOR RESIDUE SO4 B 1008
09AC9SOFTWAREHIS A:162 , ASN B:91 , SER B:93 , GLU B:95 , TRP B:96 , ARG B:99BINDING SITE FOR RESIDUE SO4 B 1009
10BC1SOFTWAREALA B:69 , GLU B:70 , SER B:71 , HOH B:1025 , HOH B:1034 , HOH B:1141BINDING SITE FOR RESIDUE SO4 B 1010
11BC2SOFTWAREGLN B:58 , ARG B:177 , HOH B:1119 , HOH B:1138BINDING SITE FOR RESIDUE SO4 B 1011
12BC3SOFTWAREGLU A:115 , VAL B:39 , ALA B:40 , HOH B:1182BINDING SITE FOR RESIDUE NA A 3001
13BC4SOFTWARELYS A:13 , HIS A:20 , GLU A:24 , LEU A:33 , ARG A:117 , TYR A:130 , VAL A:131 , GLY A:135 , SER A:138 , VAL A:142 , LYS A:173 , ARG A:177 , PHE A:201 , ASN A:204 , PHE A:208 , SO4 A:1004 , HOH A:3005 , HOH A:3017 , HOH A:3107 , HOH A:3138BINDING SITE FOR RESIDUE HEM A 901
14BC5SOFTWARELYS B:13 , HIS B:20 , GLN B:58 , TYR B:130 , VAL B:131 , GLY B:135 , SER B:138 , ARG B:177 , PHE B:201 , PHE B:208 , HOH B:1032 , HOH B:1059 , HOH B:1091 , HOH B:1196BINDING SITE FOR RESIDUE HEM B 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HMUO_CORDI125-135
 		  2A:125-135
B:125-135
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HMUO_CORDI125-135
 		  1A:125-135
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEME_OXYGENASEPS00593 Heme oxygenase signature.HMUO_CORDI125-135
 		  1-
B:125-135

(-) Exons   (0, 0)

(no "Exon" information available for 1WNX)

(-) Sequences/Alignments

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 d1wnxa_ A: Heme oxygenase HmuO                                                                                                                                                                                  SCOP domains
               CATH domains 1wnxA00 A:7-213 Heme Oxygenase; Chain A                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------HEME_OXYGEN------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wnx A   7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGELSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 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
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
           HMUO_CORDI     3 TATAGLAVELKQSTAQAHEKAEHSTFMSDLLEGRLGVAEFTRLQEQAWLFYTALEQAADAVRASGFAESLLDPALNRAEVLARDLDKLNDGSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQRENLLKEATDAFVFNHQVFADLG 212
               SCOP domains d1wnxb_ B: Heme oxygenase HmuO                                                                                                                                                                                     SCOP domains
               CATH domains 1wnxB00 B:3-212 Heme Oxygenase; Chain A                                                                                                                                                                            CATH domains
           Pfam domains (1) ---Heme_oxygenase-1wnxB01 B:6-210                                                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) ---Heme_oxygenase-1wnxB02 B:6-210                                                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------HEME_OXYGEN----------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wnx B   3 TATAGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGELSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLG 212
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HO (49)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

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