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(-) Description

Title :  ROLE OF THE BIRADICAL INTERMEDIATE OBSERVED DURING THE TURNOVER OF SLAC: A TWO-DOMAIN LACCASE FROM STREPTOMYCES COELICOLOR
 
Authors :  I. Nederlof, A. Gupta, G. W. Canters
Date :  05 Sep 12  (Deposition) - 19 Sep 12  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Two-Domain Lacasse, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gupta, I. Nederlof, S. Sottini, A. W. Tepper, E. J. Groenen, E. A. Thomassen, G. W. Canters
Involvement Of Tyr108 In The Enzyme Mechanism Of The Small Laccase From Streptomyces Coelicolor
J. Am. Chem. Soc. V. 134 18213 2012
PubMed-ID: 23094962  |  Reference-DOI: 10.1021/JA3088604

(-) Compounds

Molecule 1 - PUTATIVE COPPER OXIDASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 39-316
    Gene: SCO6712
    Mutation: YES
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 100226
    Strain: A3(2)
    Synonym: SMALL LACCASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1CU12Ligand/IonCOPPER (II) ION
2O3Ligand/IonOXYGEN ATOM
3PG43Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:231 , CYS A:288 , HIS A:293 , MET A:298BINDING SITE FOR RESIDUE CU A 401
02AC2SOFTWAREHIS A:236 , HIS A:287 , CU A:403 , HIS C:158 , O C:402BINDING SITE FOR RESIDUE CU A 402
03AC3SOFTWAREHIS A:234 , HIS A:236 , CU A:402 , HIS C:102 , HIS C:104 , CU C:401 , O C:402BINDING SITE FOR RESIDUE CU A 403
04AC4SOFTWAREHIS A:104 , HIS A:156 , CU A:405 , O A:406 , HIS B:289BINDING SITE FOR RESIDUE CU A 404
05AC5SOFTWAREHIS A:102 , HIS A:104 , CU A:404 , O A:406 , HIS B:234 , HIS B:236BINDING SITE FOR RESIDUE CU A 405
06AC6SOFTWAREHIS A:102 , HIS A:156 , HIS A:158 , CU A:404 , CU A:405 , HIS B:236 , HIS B:287 , HIS B:289 , CU B:402BINDING SITE FOR RESIDUE O A 406
07AC7SOFTWAREARG A:49 , LEU A:78 , ILE A:79 , GLU A:80BINDING SITE FOR RESIDUE PG4 A 407
08AC8SOFTWAREHIS B:231 , CYS B:288 , HIS B:293 , MET B:298BINDING SITE FOR RESIDUE CU B 401
09AC9SOFTWAREHIS A:158 , O A:406 , HIS B:236 , HIS B:287BINDING SITE FOR RESIDUE CU B 402
10BC1SOFTWAREHIS B:104 , HIS B:156 , O B:404 , HIS C:289 , CU C:405BINDING SITE FOR RESIDUE CU B 403
11BC2SOFTWAREHIS B:102 , HIS B:156 , HIS B:158 , CU B:403 , HOH B:577 , HIS C:234 , HIS C:236 , HIS C:287 , HIS C:289 , CU C:404 , CU C:405BINDING SITE FOR RESIDUE O B 404
12BC3SOFTWAREARG B:49 , LEU B:78 , ILE B:79 , GLU B:80BINDING SITE FOR RESIDUE PG4 B 405
13BC4SOFTWAREHIS A:289 , CU A:403 , HIS C:104 , HIS C:156 , O C:402BINDING SITE FOR RESIDUE CU C 401
14BC5SOFTWAREHIS A:234 , HIS A:287 , HIS A:289 , CU A:402 , CU A:403 , HIS C:102 , HIS C:156 , HIS C:158 , CU C:401 , HOH C:532BINDING SITE FOR RESIDUE O C 402
15BC6SOFTWAREHIS C:231 , CYS C:288 , HIS C:293 , MET C:298BINDING SITE FOR RESIDUE CU C 403
16BC7SOFTWAREHIS B:158 , O B:404 , HIS C:236 , HIS C:287 , CU C:405BINDING SITE FOR RESIDUE CU C 404
17BC8SOFTWAREHIS B:102 , HIS B:104 , CU B:403 , O B:404 , HIS C:234 , HIS C:236 , CU C:404BINDING SITE FOR RESIDUE CU C 405
18BC9SOFTWAREARG C:49 , LEU C:78 , ILE C:79 , GLU C:80BINDING SITE FOR RESIDUE PG4 C 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GY4)

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Ala A:42 -Pro A:43
2Gly A:45 -Gly A:46
3Val A:74 -Pro A:75
4Gly A:208 -Pro A:209
5Ala B:42 -Pro B:43
6Val B:74 -Pro B:75
7Gly B:208 -Pro B:209
8Pro B:312 -Gly B:313
9Gly C:45 -Gly C:46
10Val C:74 -Pro C:75
11Gly C:208 -Pro C:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GY4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GY4)

(-) Exons   (0, 0)

(no "Exon" information available for 4GY4)

(-) 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:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeeeee.....eeee............eeee...eeeeeeee........ee.....hhhhh.............eeeeeee....ee.....ee....eeeeee........hhhhhhhh.eeeeeee........eeeeeeee..ee..........eeee...eeeeeeeee....eeeee....ee...............ee.eeee....eeeeeee.......eeeeeee.hhhhhhh..eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gy4 A  39 ARTAPAGGEVRHLKMYAEKLADGQMGYGFEKGKASVPGPLIEVNEGDTLHIEFTNTMDVRASLHVHGLDAEISSDGTAMNKSDVEPGGTRTYTWRTHKPGRRDDGTWRPGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDATHTIVFNDMTINNRKPHTGPDFEATVGDRVEIVMITHGEYYHTFHMHGHRWADNRTGILTGPDDPSRVIDNKITGPADSFGFQIIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGY 314
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308      


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeee.....eeee............eeee...eeeeeeee........ee.....hhhhh.............eeeeeee....ee.....ee....eeeeee........hhhhhhhh.eeeeeee........eeeeeeee..ee..........eeee...eeeeeeeee....eeeee....ee...............ee.eeee....eeeeeee.......eeeeeee.hhhhhhh..eeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gy4 B  39 ARTAPAGGEVRHLKMYAEKLADGQMGYGFEKGKASVPGPLIEVNEGDTLHIEFTNTMDVRASLHVHGLDAEISSDGTAMNKSDVEPGGTRTYTWRTHKPGRRDDGTWRPGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDATHTIVFNDMTINNRKPHTGPDFEATVGDRVEIVMITHGEYYHTFHMHGHRWADNRTGILTGPDDPSRVIDNKITGPADSFGFQIIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGYEP 316
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        


Chain C from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeee.....eeee............eeee...eeeeeeee........ee.....hhhhh.............eeeeeee....ee.....ee....eeeeee........hhhhhhhh.eeeeeee........eeeeeeee..ee..........eeee...eeeeeeeee....eeeee....ee...............ee.eeee....eeeeeee.......eeeeeee.hhhhhhh..eeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gy4 C  39 ARTAPAGGEVRHLKMYAEKLADGQMGYGFEKGKASVPGPLIEVNEGDTLHIEFTNTMDVRASLHVHGLDAEISSDGTAMNKSDVEPGGTRTYTWRTHKPGRRDDGTWRPGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDATHTIVFNDMTINNRKPHTGPDFEATVGDRVEIVMITHGEYYHTFHMHGHRWADNRTGILTGPDDPSRVIDNKITGPADSFGFQIIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGYEP 316
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308
   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 4GY4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GY4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GY4)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Gly A:45 - Gly A:46   [ RasMol ]  
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    Pro B:312 - Gly B:313   [ RasMol ]  
    Val A:74 - Pro A:75   [ RasMol ]  
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    Val C:74 - Pro C:75   [ RasMol ]  
 

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 Related Entries

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        Q9XAL8_STRCO | Q9XAL8: 3cg8 3kw8 4gxf

(-) Related Entries Specified in the PDB File

4gxf SAME PROTEIN Y108F