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(-) Description

Title :  STRUCTURAL AND KINETIC STUDY OF AN INTERNAL SUBSTRATE BINDING SITE OF DEHALOPEROXIDASE-HEMOGLOBIN A FROM AMPHITRITE ORNATA
 
Authors :  V. S. De Serrano, J. Zhao, J. Zhao, S. Franzen
Date :  01 Jan 13  (Deposition) - 27 Mar 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Peroxidase, Globin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhao, V. De Serrano, J. Zhao, P. Le, S. Franzen
Structural And Kinetic Study Of An Internal Substrate Binding Site In Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata.
Biochemistry V. 52 2427 2013
PubMed-ID: 23480178  |  Reference-DOI: 10.1021/BI301307F

(-) Compounds

Molecule 1 - DEHALOPEROXIDASE A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DHPA
    Organism Scientific: AMPHITRITE ORNATA
    Organism Taxid: 129555

 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  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IPA7Ligand/IonISOPROPYL ALCOHOL
3OXY1Ligand/IonOXYGEN MOLECULE
4SO44Ligand/IonSULFATE ION
5TBP1Ligand/Ion2,4,6-TRIBROMOPHENOL
Biological Unit 1 (5, 15)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IPA7Ligand/IonISOPROPYL ALCOHOL
3OXY1Ligand/IonOXYGEN MOLECULE
4SO44Ligand/IonSULFATE ION
5TBP1Ligand/Ion2,4,6-TRIBROMOPHENOL
Biological Unit 2 (5, 12)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IPA7Ligand/IonISOPROPYL ALCOHOL
3OXY1Ligand/IonOXYGEN MOLECULE
4SO42Ligand/IonSULFATE ION
5TBP1Ligand/Ion2,4,6-TRIBROMOPHENOL
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IPA-1Ligand/IonISOPROPYL ALCOHOL
3OXY-1Ligand/IonOXYGEN MOLECULE
4SO42Ligand/IonSULFATE ION
5TBP-1Ligand/Ion2,4,6-TRIBROMOPHENOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:24 , GLU A:31 , TYR A:34 , PHE A:35 , HIS A:55 , LYS A:58 , VAL A:59 , MET A:63 , LEU A:83 , MET A:86 , GLN A:88 , HIS A:89 , LEU A:92 , ASN A:96 , PHE A:97 , TBP A:211 , OXY A:212 , HOH A:335BINDING SITE FOR RESIDUE HEM A 201
02AC2SOFTWAREGLY A:1 , PHE A:2 , LYS A:3 , ASP A:116 , HOH A:305 , HOH A:312 , HOH A:330 , ARG B:32 , GLY B:40BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWAREARG A:32 , VAL A:39 , GLY A:40 , IPA A:204 , IPA A:209 , HOH A:344 , GLY B:1 , PHE B:2 , LYS B:3 , ASP B:116 , HOH B:311 , HOH B:318BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWARELEU A:25 , PRO A:29 , ARG A:32 , SO4 A:203 , GLY B:1 , ASP B:116BINDING SITE FOR RESIDUE IPA A 204
05AC5SOFTWARESER A:111 , GLY A:112BINDING SITE FOR RESIDUE IPA A 205
06AC6SOFTWAREMET A:108 , ARG A:109 , SER A:111 , GLN A:113 , SER A:114 , PHE A:115 , IPA A:208 , HOH A:366BINDING SITE FOR RESIDUE IPA A 206
07AC7SOFTWARELEU A:76 , ALA A:77 , HOH A:353 , HOH B:351 , HOH B:352BINDING SITE FOR RESIDUE IPA A 207
08AC8SOFTWARESER A:114 , PHE A:115 , IPA A:206 , LYS B:27 , HOH B:347BINDING SITE FOR RESIDUE IPA A 208
09AC9SOFTWAREARG A:32 , LYS A:41 , SER A:42 , ASP A:43 , LEU A:46 , SO4 A:203 , HOH A:345 , GLN B:4 , HOH B:318BINDING SITE FOR RESIDUE IPA A 209
10BC1SOFTWARETYR A:28 , PRO A:29 , ASP A:30 , HOH A:393 , HOH A:394 , ARG B:33BINDING SITE FOR RESIDUE IPA A 210
11BC2SOFTWAREILE A:20 , PHE A:21 , PHE A:24 , PHE A:35 , VAL A:59 , PHE A:60 , MET A:63 , LEU A:100 , HEM A:201 , OXY A:212BINDING SITE FOR RESIDUE TBP A 211
12BC3SOFTWAREHIS A:55 , VAL A:59 , HEM A:201 , TBP A:211BINDING SITE FOR RESIDUE OXY A 212
13BC4SOFTWAREGLU B:31 , TYR B:34 , PHE B:35 , LYS B:36 , HIS B:55 , LYS B:58 , VAL B:59 , MET B:63 , LEU B:83 , MET B:86 , GLN B:88 , HIS B:89 , LEU B:92 , ASN B:96 , PHE B:97 , LEU B:127 , HOH B:344BINDING SITE FOR RESIDUE HEM B 201
14BC5SOFTWARELYS A:99 , HOH A:329 , ASP B:30 , GLU B:31 , ARG B:33 , TYR B:34 , ASN B:96 , LYS B:99 , HOH B:338 , HOH B:377BINDING SITE FOR RESIDUE SO4 B 202
15BC6SOFTWAREARG A:33 , TYR A:34 , GLN A:118 , LYS B:27 , TYR B:28 , PRO B:29 , ASP B:30 , HOH B:346 , HOH B:364 , HOH B:392BINDING SITE FOR RESIDUE SO4 B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ILZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ILZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ILZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ILZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4ILZ)

(-) 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
                                                                                                                                                                         
               SCOP domains d4ilza_ A: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilz 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
                                                                                                                                                                         
               SCOP domains d4ilzb_ B: Dehaloperoxidase                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilz 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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  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  (0, 0)

(no "CATH Domain" information available for 4ILZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ILZ)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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

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