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(-) Description

Title :  CRYSTAL STRUCTURE OF A DYE-DECOLORIZING PEROXIDASE (DYP) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.6 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  02 May 06  (Deposition) - 16 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Pc04261D, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Heme Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zubieta, S. S. Krishna, M. Kapoor, P. Kozbial, D. Mcmullan, H. L. Axelrod, M. D. Miller, P. Abdubek, E. Ambing, T. Astakhova, D. Carlton, H. J. Chiu, T. Clayton, M. C. Deller, L. Duan, M. A. Elsliger J. Feuerhelm, S. K. Grzechnik, J. Hale, E. Hampton, G. W. Han, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, A. Kumar, D. Marciano, A. T. Morse, E. Nigoghossian, L. Okach, S. Oommachen, R. Reyes, C. L. Rife, P. Schimmel, H. Van Den Bedem, D. Weekes, A. White, Q. Xu, K. O. Hodgson, J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Crystal Structures Of Two Novel Dye-Decolorizing Peroxidase Reveal A Beta-Barrel Fold With A Conserved Heme-Binding Motif.
Proteins V. 69 223 2007
PubMed-ID: 17654545  |  Reference-DOI: 10.1002/PROT.21550

(-) Compounds

Molecule 1 - HEME PEROXIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BT_1219
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 22)

Asymmetric Unit (6, 22)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2CL3Ligand/IonCHLORIDE ION
3EDO5Ligand/Ion1,2-ETHANEDIOL
4MSE10Mod. Amino AcidSELENOMETHIONINE
5NA1Ligand/IonSODIUM ION
6UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (4, 108)
No.NameCountTypeFull Name
1ACY12Ligand/IonACETIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO30Ligand/Ion1,2-ETHANEDIOL
4MSE60Mod. Amino AcidSELENOMETHIONINE
5NA-1Ligand/IonSODIUM ION
6UNL6Ligand/IonUNKNOWN LIGAND

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:59 , PRO A:60 , ASP A:61BINDING SITE FOR RESIDUE CL A 317
02AC2SOFTWARESER A:92 , ARG A:273 , HOH A:446BINDING SITE FOR RESIDUE CL A 318
03AC3SOFTWAREPHE A:79 , PRO A:80 , ASP A:81BINDING SITE FOR RESIDUE CL A 319
04AC4SOFTWAREPRO A:35 , ASP A:36 , ASP A:81 , HOH A:371 , HOH A:438 , HOH A:481BINDING SITE FOR RESIDUE NA A 320
05AC5SOFTWAREGLN A:20 , ASN A:57 , ARG A:145 , TYR A:146 , GLY A:149 , LYS A:150 , ASP A:157 , ASN A:247 , PRO A:249 , HOH A:331BINDING SITE FOR RESIDUE UNL A 321
06AC6SOFTWARETHR A:104 , PRO A:105 , VAL A:138 , VAL A:189 , THR A:299 , THR A:301 , HOH A:432 , HOH A:436BINDING SITE FOR RESIDUE EDO A 322
07AC7SOFTWAREHIS A:231 , ARG A:245 , ASN A:247 , PHE A:262 , MSE A:275 , MSE A:279 , ACY A:327 , HOH A:530BINDING SITE FOR RESIDUE EDO A 323
08AC8SOFTWAREALA A:72 , ASP A:73 , THR A:90 , GLY A:106 , HOH A:338 , HOH A:345BINDING SITE FOR RESIDUE EDO A 324
09AC9SOFTWAREASP A:128 , LYS A:132 , SER A:254 , LYS A:255 , GLY A:256 , HOH A:359BINDING SITE FOR RESIDUE EDO A 325
10BC1SOFTWAREHIS A:170 , LEU A:241 , SER A:267 , HOH A:420BINDING SITE FOR RESIDUE EDO A 326
11BC2SOFTWAREHIS A:194 , ASN A:247 , LEU A:291 , EDO A:323 , HOH A:644BINDING SITE FOR RESIDUE ACY A 327
12BC3SOFTWAREASP A:148BINDING SITE FOR RESIDUE ACY A 328

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:283 -Pro A:284

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GVK)

(-) 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:309
 aligned with Q8A8E8_BACTN | Q8A8E8 from UniProtKB/TrEMBL  Length:316

    Alignment length:309
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307         
         Q8A8E8_BACTN     8 FGGHIPQDVAGKQGENVIFIVYNLTDSPDTVDKVKDVCANFSAMIRSMRNRFPDMQFSCTMGFGADAWTRLFPDKGKPKELSTFSEIKGEKYTAVSTPGDLLFHIRAKQMGLCFEFASILDEKLKGAVVSVDETHGFRYMDGKAIIGFVDGTENPAVDENPYHFAVIGEEDADFAGGSYVFVQKYIHDMVAWNALPVEQQEKVIGRHKFNDVELSDEEKPGNAHNAVTNIGDDLKIVRANMPFANTSKGEYGTYFIGYASTFSTTRRMLENMFIGSPAGNTDRLLDFSTAITGTLFFVPSYDLLGELGE 316
               SCOP domains d2gvka1 A:8-316 Hypothetical protein BT1219                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhhhh..............ee....ee......eeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeeee......................hhhhhhh.hhhhhhhh..eeeeeeeeeehhhhhhh.hhhhhhhhhh.................hhhhhh........eeeeeeeeehhhheeeeeeeeee.hhhhhhhhhhhhhh.......hhhhh.eee...eeeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gvk A   8 FGGHIPQDVAGKQGENVIFIVYNLTDSPDTVDKVKDVCANFSAmIRSmRNRFPDmQFSCTmGFGADAWTRLFPDKGKPKELSTFSEIKGEKYTAVSTPGDLLFHIRAKQmGLCFEFASILDEKLKGAVVSVDETHGFRYmDGKAIIGFVDGTENPAVDENPYHFAVIGEEDADFAGGSYVFVQKYIHDmVAWNALPVEQQEKVIGRHKFNDVELSDEEKPGNAHNAVTNIGDDLKIVRANmPFANTSKGEYGTYFIGYASTFSTTRRmLENmFIGSPAGNTDRLLDFSTAITGTLFFVPSYDLLGELGE 316
                                    17        27        37        47   |   |57    |   67|       77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247|      257       267       277 |     287       297       307         
                                                                      51-MSE     62-MSE |                                              117-MSE                       147-MSE                                          196-MSE                                             248-MSE                    275-MSE                                     
                                                                          55-MSE       68-MSE                                                                                                                                                                                                            279-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GVK)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8A8E8_BACTN | Q8A8E8)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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: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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