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(-) Description

Title :  CRYSTAL STRUCTURE OF GEOBACTER METALLIREDUCENS SMUG1 WITH XANTHINE
 
Authors :  W. Xie, W. Cao, Z. Zhang, J. Shen
Date :  28 Dec 15  (Deposition) - 27 Apr 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Smug1, Dna Damage, Base Excision Repair, Substrate Specificity, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, J. Shen, Y. Yang, J. Li, W. Cao, W. Xie
Structural Basis Of Substrate Specificity In Geobacter Metallireducens Smug1
Acs Chem. Biol. V. 11 1729 2016
PubMed-ID: 27071000  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00164

(-) Compounds

Molecule 1 - GEOBACTER METALLIREDUCENS SMUG1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GMET_0095
    Organism Scientific: GEOBACTER METALLIREDUCENS (STRAIN GS-15 / ATCC 53774 / DSM 7210)
    Organism Taxid: 269799
    Strain: GS-15 / ATCC 53774 / DSM 7210

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2GOL3Ligand/IonGLYCEROL
3IPA1Ligand/IonISOPROPYL ALCOHOL
4LEA1Ligand/IonPENTANOIC ACID
5XAN1Ligand/IonXANTHINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:57 , ASN A:58 , PRO A:70 , PHE A:71 , GLU A:108 , SER A:110 , ASN A:136 , HIS A:210 , HOH A:428 , HOH A:476binding site for residue XAN A 301
2AC2SOFTWARELEU A:32 , TYR A:33 , ALA A:34 , ARG A:35 , GLU A:36 , PRO A:37 , THR A:86 , THR A:88binding site for residue GOL A 302
3AC3SOFTWAREGLU A:36 , PRO A:37 , ARG A:44 , ILE A:83 , ASN A:84 , GLY A:85 , PRO A:125 , HOH A:409 , HOH A:412 , HOH A:420binding site for residue GOL A 303
4AC4SOFTWAREPRO A:-1 , ALA A:10 , ASP A:14 , ARG A:89 , LEU A:169 , ARG A:173binding site for residue GOL A 304
5AC5SOFTWAREGLY A:85 , THR A:86 , VAL A:87 , ASP A:100 , PHE A:102binding site for residue BME A 305
6AC6SOFTWARETHR A:78 , GLU A:79 , GLY A:82 , ASN A:84binding site for residue IPA A 306
7AC7SOFTWAREARG A:121 , PHE A:122 , ARG A:127 , ARG A:131 , LEU A:227 , ALA A:231 , VAL A:235 , PHE A:237binding site for residue LEA A 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H9I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:22 -Pro A:23
2Pro A:48 -Pro A:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H9I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H9I)

(-) Exons   (0, 0)

(no "Exon" information available for 5H9I)

(-) 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:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh........eeehhhhhhhhhhhhhhhhhh.....eeeee......hhhhhh....hhhhhhhh...................hhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eeeee....eee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5h9i A  -2 GPHMTGLAAISDALAADLAGLSFSSPVAHVYNPLLYAREPHVAYLSRFGSPPKEVLFVGMNPGPWGMAQTGVPFGEVAVVTEWLGINGTVTRPAGEHPKKRVDGFACRRSEVSGRRLWGFIRERFGTPERFFARFFVANYCPLLFLTAEGGNITPDKLRRGEQEPLFAACDLALRRTVVLLRPRVVIGVGAFAEARCHEALEGFDVEVGRIIHPSPASPAANRDWAGTALRQLAELGVDF 237
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237
   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  (0, 0)

(no "SCOP Domain" information available for 5H9I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H9I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H9I)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5H9I)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/TrEMBL
        Q39ZI0_GEOMG | Q39ZI0: 5h93 5h98 5h99

(-) Related Entries Specified in the PDB File

5h93 5h98 5h99