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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ARTIFICIAL METALLOPROTEIN: CR[N-SALICYLIDENE-4-AMINO-3-HYDROXYHYDROCINNAMIC ACID]/WILD TYPE HEME OXYGENASE
 
Authors :  N. Yokoi, M. Unno, T. Ueno, M. Ikeda-Saito, Y. Watanabe
Date :  24 Jul 07  (Deposition) - 28 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Electron-Transfer, Metal, Artificial Metalloprotein, Heme Oxygenase, Salophen, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Yokoi, T. Ueno, M. Unno, T. Matsui, M. Ikeda-Saito, Y. Watanabe
Ligand Design For Improvement Of Thermal Stabilityof Metal Complex/Protein Hybrids
To Be Published
PubMed: search
(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 BL21(DE3)
    Expression System Plasmid: PMW172-A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    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, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2SO43Ligand/IonSULFATE ION
3TIL2Ligand/Ion[2-[5-CARBOXYETHYL-2-PHENOLATO(NITRILOMETHYLIDYNE)][PHENOLATO]]CHROMIUM(III)
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2SO42Ligand/IonSULFATE ION
3TIL1Ligand/Ion[2-[5-CARBOXYETHYL-2-PHENOLATO(NITRILOMETHYLIDYNE)][PHENOLATO]]CHROMIUM(III)
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2SO41Ligand/IonSULFATE ION
3TIL1Ligand/Ion[2-[5-CARBOXYETHYL-2-PHENOLATO(NITRILOMETHYLIDYNE)][PHENOLATO]]CHROMIUM(III)

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:26 , THR A:27 , HIS A:205 , ALA A:209 , HOH A:952BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWARESER B:26 , THR B:27 , HIS B:205 , ALA B:209 , HOH B:1064BINDING SITE FOR RESIDUE SO4 B 702
3AC3SOFTWAREALA A:69 , GLU A:70 , SER A:71 , HOH A:946 , HOH A:1033BINDING SITE FOR RESIDUE SO4 A 703
4AC4SOFTWARELYS A:170 , ASP A:174 , ARG A:177BINDING SITE FOR RESIDUE NA A 601
5AC5SOFTWAREASP B:121 , HIS B:192 , GLU B:196 , HOH B:983 , HOH B:1105BINDING SITE FOR RESIDUE NA B 602
6AC6SOFTWAREHIS A:20 , GLU A:24 , TYR A:130 , VAL A:131 , ARG A:132 , LEU A:134 , GLY A:135 , SER A:138 , ARG A:177 , PHE A:201 , ASN A:204 , HOH A:993 , HOH A:1049 , HOH A:1115BINDING SITE FOR RESIDUE TIL A 901
7AC7SOFTWAREHIS B:20 , GLU B:24 , TYR B:130 , VAL B:131 , LEU B:134 , GLY B:135 , ARG B:177 , PHE B:201 , ASN B:204 , HOH B:947 , HOH B:1117 , HOH B:1119 , HOH B:1120BINDING SITE FOR RESIDUE TIL B 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z68)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z68)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z68)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z68)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z68)

(-) 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:209
 aligned with Q54AI1_CORDP | Q54AI1 from UniProtKB/TrEMBL  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         
         Q54AI1_CORDP     7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL 215
               SCOP domains d2z68a_ A: Heme oxygenase HmuO                                                                                                                                                                                    SCOP domains
               CATH domains 2z68A00 A:7-215 Heme Oxygenase; Chain A                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z68 A   7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL 215
                                    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:208
 aligned with Q54AI1_CORDP | Q54AI1 from UniProtKB/TrEMBL  Length:215

    Alignment length:208
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        
         Q54AI1_CORDP     7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKG 214
               SCOP domains d2z68b_ B: Heme oxygenase HmuO                                                                                                                                                                                   SCOP domains
               CATH domains 2z68B00 B:7-214 Heme Oxygenase; Chain A                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z68 B   7 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKG 214
                                    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)
    → 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  (0, 0)

(no "Pfam Domain" information available for 2Z68)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q54AI1_CORDP | Q54AI1)
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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  2z68
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 Related Entries

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UniProtKB/TrEMBL
        Q54AI1_CORDP | Q54AI1: 1wzd 3i8r 3moo 4goh 4gpc 4gpf 4gph

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