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(-) Description

Title :  SPORE PHOTOPRODUCT LYASE Y98F MUTANT
 
Authors :  L. Yang, R. S. Nelson, A. Benjdia, G. Lin, J. Telser, S. Stoll, I. Schlich
Date :  20 Apr 13  (Deposition) - 08 May 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Partial Tim Barrel, Dna Repair, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Yang, R. S. Nelson, A. Benjdia, G. Lin, J. Telser, S. Stoll, I. Schlichting, L. Li
A Radical Transfer Pathway In Spore Photoproduct Lyase.
Biochemistry V. 52 3041 2013
PubMed-ID: 23607538  |  Reference-DOI: 10.1021/BI3016247

(-) Compounds

Molecule 1 - SPORE PHOTOPRODUCT LYASE
    Chains: A
    EC Number: 4.1.99.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GTNG_2348
    Mutation: YES
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS
    Organism Taxid: 420246
    Strain: NG80-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1EEM1Ligand/Ion[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM
2SF41Ligand/IonIRON/SULFUR CLUSTER
3SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:90 , GLY A:92 , CYS A:94 , CYS A:97 , LEU A:99 , LYS A:174 , EEM A:402BINDING SITE FOR RESIDUE SF4 A 401
2AC2SOFTWARETYR A:96 , CYS A:97 , PHE A:98 , ALA A:139 , SER A:142 , ASP A:143 , VAL A:172 , LYS A:174 , SER A:195 , VAL A:232 , ALA A:234 , PRO A:235 , GLN A:271 , HIS A:272 , ARG A:273 , SF4 A:401BINDING SITE FOR RESIDUE EEM A 402
3AC3SOFTWAREARG A:135 , ARG A:170 , ARG A:191 , LYS A:228 , GLN A:338 , HOH A:578BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREARG A:36BINDING SITE FOR RESIDUE SO4 A 404
5AC5SOFTWAREARG A:68 , THR A:88 , THR A:141 , HOH A:539BINDING SITE FOR RESIDUE SO4 A 405
6AC6SOFTWAREARG A:304 , TYR A:305 , GLY A:306BINDING SITE FOR RESIDUE SO4 A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K9R)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:77 -Pro A:78
2Ala A:130 -Pro A:131
3Ala A:234 -Pro A:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K9R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K9R)

(-) Exons   (0, 0)

(no "Exon" information available for 4K9R)

(-) 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:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.hhhhhhhhhhhhhhhhhhhh.eeee.............hhhhhhhhhh.eeeee...............ee...ee........hhhhhh......eeee.hhhhhhhhhhhhhhhhh...eeee.....hhhhhhh..hhhhhhhhhhhhh..eeeeeee....hhhhh.......eeeeeee.hhhhhhhhh....hhhhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhh.........eeeeee.....hhhhhhhhhh.......hhh.eeee.......eeeehhhhhhhhhhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9r A   2 KPFVPKLVYFEPEALSYPLGKELYEKFTQMGIKIRETTSHNQVRGIPGETELARYRNAKSTLVVGVRRTLKFDSSKPSAEYAIPLATGCMGHCHYCFLQTTLGSKPYIRVYVNLDDIFAQAQKYINERAPEITRFEAACTSDIVGIDHLTHSLKKAIEFIGATDYGRLRFVTKYEHVDHLLDARHNGKTRFRFSINSRYVINHFEPGTSSFDGRLAAARKVAGAGYKLGFVVAPIYRHEGWERGYFELFQELARQLEGMDLSDLTFELIQHRFTKPAKRVIEQRYPKTRLDLDETKRKYKWGRYGIGKYVYRDEEAKELEDTMRRYIEQFFPGAYVQYFT 341
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341
   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 4K9R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K9R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K9R)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:130 - Pro A:131   [ RasMol ]  
    Ala A:234 - Pro A:235   [ RasMol ]  
    Lys A:77 - Pro A:78   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        A4IQU1_GEOTN | A4IQU1: 4fhc 4fhd 4fhe 4fhf 4fhg 4rh0 4rh1

(-) Related Entries Specified in the PDB File

4fhc SPORE PHOTOPRODUCT LYASE