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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF APO-TYPE BACTERIAL VANADIUM-DEPENDENT CHLOROPEROXIDASE
 
Authors :  D. K. Liscombe, A. Miyanaga, E. Fielding, P. Bernhardt, A. Li, J. M. Wint M. K. Gilson, J. P. Noel, B. S. Moore
Date :  11 Dec 12  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chloroperoxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Liscombe, A. Miyanaga, E. Fielding, P. Bernhardt, A. Li, J. M. Winter, M. K. Gilson, J. P. Noel, B. S. Moore
Structure-Function Analysis Of A Bacterial Vanadium-Dependent Chloroperoxidase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NAPH1
    Chains: A, B
    EC Number: 1.11.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NAPH1
    Organism Scientific: STREPTOMYCES
    Organism Taxid: 445602
    Strain: CNQ525
    Synonym: VANADIUM-DEPENDENT CHLOROPEROXIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3W35)

(-) Sites  (0, 0)

(no "Site" information available for 3W35)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W35)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Gln A:152 -Gln A:153
2Gly A:197 -Met A:198
3Asn A:342 -Asn A:343
4Tyr A:423 -Pro A:424
5Thr A:465 -Pro A:466
6Asn B:342 -Asn B:343
7Met B:345 -Gly B:346
8Tyr B:423 -Pro B:424
9Thr B:465 -Pro B:466

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W35)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W35)

(-) Exons   (0, 0)

(no "Exon" information available for 3W35)

(-) Sequences/Alignments

Asymmetric/Biological 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:459
 aligned with A7KH27_9ACTN | A7KH27 from UniProtKB/TrEMBL  Length:527

    Alignment length:468
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515        
         A7KH27_9ACTN    56 FDLDKDNYIKWAQPTDENAGQSPTLAILGPMDVTVFLWINRVVWLAAFDALAPYHETAVGVYSQIPRRPSSESATNRNLNIAALHAQHGVWKRVLPQQVDQLRELMTALGLDPSDETENLSSPVGIGNVAAKNAFNALKNDGMNFLGYEGRKYNPRPWADYTGYEPVNTAFKVNNPSRWQPQLQAHNARRAGGGPGDLGIYVTQHFVTPQTARTKAHIFRDPSRFRIPRPEFSDHTNTRAYKRSVDEIIDASANLNDERKALAEIMENKLWGIGHSSIVIANKYDQNNEMGVHGWCHWMLAHVLATFEPLIAAWHHKTRFDAVRPVTAIRHVYGNRKIRAWGGVGMGTVDIRASEWSSYLPVGDHPEYPSGSTSLCSATSQAARRYFDSDELDWTINYPAGSTVVEPGITPGKDLSIHIPTWTDFTRTCATSRVWGGVHFQTTVDRTIDFGEQFGDLAHEFVQRHVKG 523
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhh.---------.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.............hhhhhhhhhhhhhhhhhh...........................................eee...............eeee...hhhhhhh......hhhhh....hhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..eeeee......eeeee.hhh.............hhhhhhhhhhhhhhhhhhh..eeeeeeee................eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w35 A  56 FDLDKDNYIKWAQ---------PTLAILGPMDVTVFLWINRVVWLAAFDALAPYHETAVGVYSQIPRRPSSESATNRNLNIAALHAQHGVWKRVLPQQVDQLRELMTALGLDPSDETENLSSPVGIGNVAAKNAFNALKNDGMNFLGYEGRKYNPRPWADYTGYEPVNTAFKVNNPSRWQPQLQAHNARRAGGGPGDLGIYVTQHFVTPQTARTKAHIFRDPSRFRIPRPEFSDHTNTRAYKRSVDEIIDASANLNDERKALAEIMENKLWGIGHSSIVIANKYDQNNEMGVHGWCHWMLAHVLATFEPLIAAWHHKTRFDAVRPVTAIRHVYGNRKIRAWGGVGMGTVDIRASEWSSYLPVGDHPEYPSGSTSLCSATSQAARRYFDSDELDWTINYPAGSTVVEPGITPGKDLSIHIPTWTDFTRTCATSRVWGGVHFQTTVDRTIDFGEQFGDLAHEFVQRHVKG 523
                                    65  |      -  |     85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515        
                                       68        78                                                                                                                                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:463
 aligned with A7KH27_9ACTN | A7KH27 from UniProtKB/TrEMBL  Length:527

    Alignment length:470
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525
         A7KH27_9ACTN    56 FDLDKDNYIKWAQPTDENAGQSPTLAILGPMDVTVFLWINRVVWLAAFDALAPYHETAVGVYSQIPRRPSSESATNRNLNIAALHAQHGVWKRVLPQQVDQLRELMTALGLDPSDETENLSSPVGIGNVAAKNAFNALKNDGMNFLGYEGRKYNPRPWADYTGYEPVNTAFKVNNPSRWQPQLQAHNARRAGGGPGDLGIYVTQHFVTPQTARTKAHIFRDPSRFRIPRPEFSDHTNTRAYKRSVDEIIDASANLNDERKALAEIMENKLWGIGHSSIVIANKYDQNNEMGVHGWCHWMLAHVLATFEPLIAAWHHKTRFDAVRPVTAIRHVYGNRKIRAWGGVGMGTVDIRASEWSSYLPVGDHPEYPSGSTSLCSATSQAARRYFDSDELDWTINYPAGSTVVEPGITPGKDLSIHIPTWTDFTRTCATSRVWGGVHFQTTVDRTIDFGEQFGDLAHEFVQRHVKGDV 525
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh..-------..........hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh...........................................eee...............eeee...hhhhhhh......hhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..eeeee......eeeee.................hhhhhhhhhhhhhhhhhhh..eeeeeeee................eeeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w35 B  56 FDLDKDNYIKWAQP-------SPTLAILGPMDVTVFLWINRVVWLAAFDALAPYHETAVGVYSQIPRRPSSESATNRNLNIAALHAQHGVWKRVLPQQVDQLRELMTALGLDPSDETENLSSPVGIGNVAAKNAFNALKNDGMNFLGYEGRKYNPRPWADYTGYEPVNTAFKVNNPSRWQPQLQAHNARRAGGGPGDLGIYVTQHFVTPQTARTKAHIFRDPSRFRIPRPEFSDHTNTRAYKRSVDEIIDASANLNDERKALAEIMENKLWGIGHSSIVIANKYDQNNEMGVHGWCHWMLAHVLATFEPLIAAWHHKTRFDAVRPVTAIRHVYGNRKIRAWGGVGMGTVDIRASEWSSYLPVGDHPEYPSGSTSLCSATSQAARRYFDSDELDWTINYPAGSTVVEPGITPGKDLSIHIPTWTDFTRTCATSRVWGGVHFQTTVDRTIDFGEQFGDLAHEFVQRHVKGDV 525
                                    65   |     - |      85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525
                                        69      77
   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  (0, 0)

(no "SCOP Domain" information available for 3W35)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W35)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W35)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A7KH27_9ACTN | A7KH27)
molecular function
    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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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 3w35)
 
  Cis Peptide Bonds
    Asn A:342 - Asn A:343   [ RasMol ]  
    Asn B:342 - Asn B:343   [ RasMol ]  
    Gln A:152 - Gln A:153   [ RasMol ]  
    Gly A:197 - Met A:198   [ RasMol ]  
    Met B:345 - Gly B:346   [ RasMol ]  
    Thr A:465 - Pro A:466   [ RasMol ]  
    Thr B:465 - Pro B:466   [ RasMol ]  
    Tyr A:423 - Pro A:424   [ RasMol ]  
    Tyr B:423 - Pro B:424   [ RasMol ]  
 

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 Databases and Analysis Tools

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  3w35
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  A7KH27_9ACTN | A7KH27
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  1.11.1.10
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 Related Entries

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

UniProtKB/TrEMBL
        A7KH27_9ACTN | A7KH27: 3w36

(-) Related Entries Specified in the PDB File

3w36