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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE ANALYSIS OF THE BINDING SITE IN THE FERRIC AND OXYFERROUS FORMS OF THE RECOMBINANT HEME DEHALOPEROXIDASE CLONED FROM AMPHITRITE ORNATA
 
Authors :  V. S. De Serrano, Z. Chen, M. F. Davis, S. Franzen
Date :  27 Jun 07  (Deposition) - 08 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Crystal Structure Of Dehaloperoxidase, Dhp, Globin, Heme Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. S. De Serrano, Z. Chen, M. F. Davis, S. Franzen
X-Ray Crystal Structural Analysis Of The Binding Site In The Ferric And Oxyferrous Forms Of The Recombinant Heme Dehaloperoxidase Cloned From Amphitrite Ornata
Acta Crystallogr. , Sect. D V. 63 1094 2007
PubMed-ID: 17881827  |  Reference-DOI: 10.1107/S0907444907043417
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEHALOPEROXIDASE A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Vector Type: PLASMID
    Gene: DHPA
    Organism Scientific: AMPHITRITE ORNATA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NH43Ligand/IonAMMONIUM ION
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NH43Ligand/IonAMMONIUM ION
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NH42Ligand/IonAMMONIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NH41Ligand/IonAMMONIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:113 , HOH A:513 , HOH A:552BINDING SITE FOR RESIDUE NH4 A 190
2AC2SOFTWAREASP A:116 , SER A:117 , GLN A:118 , HOH A:506BINDING SITE FOR RESIDUE NH4 A 192
3AC3SOFTWAREARG B:109 , GLN B:118 , ASP B:121 , HOH B:551BINDING SITE FOR RESIDUE NH4 B 193
4AC4SOFTWAREARG A:32 , GLY A:40 , HOH A:629 , GLY B:1 , PHE B:2 , LYS B:3 , HOH B:610 , HOH B:786BINDING SITE FOR RESIDUE SO4 A 195
5AC5SOFTWAREGLY A:1 , PHE A:2 , LYS A:3 , HOH A:640 , ARG B:32 , GLY B:40 , HOH B:524 , HOH B:677BINDING SITE FOR RESIDUE SO4 B 196
6AC6SOFTWAREGLY A:95 , LYS A:99 , HOH A:671 , HOH A:758 , GLY B:95 , LYS B:99 , HOH B:681BINDING SITE FOR RESIDUE SO4 B 197
7AC7SOFTWAREGLU A:31 , TYR A:34 , PHE A:35 , HIS A:55 , LYS A:58 , VAL A:59 , MET A:63 , MET A:86 , GLN A:88 , HIS A:89 , LEU A:92 , ASN A:96 , PHE A:97 , LEU A:127 , HOH A:835BINDING SITE FOR RESIDUE HEM A 139
8AC8SOFTWAREGLU B:31 , TYR B:34 , PHE B:35 , HIS B:55 , LYS B:58 , VAL B:59 , MET B:86 , GLN B:88 , HIS B:89 , LEU B:92 , ASN B:96 , PHE B:97 , LEU B:127 , HOH B:827 , HOH B:834BINDING SITE FOR RESIDUE HEM B 139

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QFK)

(-) 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:137
 aligned with Q9NAV8_9ANNE | Q9NAV8 from UniProtKB/TrEMBL  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
         Q9NAV8_9ANNE     2 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 138
               SCOP domains d2qfka_ A: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains 2qfkA00 A:1-137 Globins                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfk A   1 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       


Chain B from PDB  Type:PROTEIN  Length:137
 aligned with Q9NAV8_9ANNE | Q9NAV8 from UniProtKB/TrEMBL  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
         Q9NAV8_9ANNE     2 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 138
               SCOP domains d2qfkb_ B: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains 2qfkB00 B:1-137 Globins                                                                                                                   CATH domains
           Pfam domains (1) -Globin-2qfkB01 B:2-128                                                                                                         --------- Pfam domains (1)
           Pfam domains (2) -Globin-2qfkB02 B:2-128                                                                                                         --------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfk B   1 GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   Legend:   → Mismatch (orange background)
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    → 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: Globin (291)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9NAV8_9ANNE | Q9NAV8)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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 Related Entries

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UniProtKB/TrEMBL
        Q9NAV8_9ANNE | Q9NAV8: 1ew6 1ewa 2qfn 3dr9 3k3u 3kun 3kuo 3lb1 3lb2 3lb3 3lb4 3mou 3mym 3myn 3o7n 3oj1 3ok5 3ord 4dwt 4dwu 4fh6 4fh7 4gzg 4hsw 4hsx 4ilz 4jac 4jyq 4kjt 4kmv 4kmw 4kn3

(-) Related Entries Specified in the PDB File

2qfn SAME PROTEIN WITH C73S MUTATION