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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE RIBOFLAVIN BIOSYNTHESIS PROTEIN (YP_001092907.1) FROM SHEWANELLA SP. PV-4 AT 2.12 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  04 Dec 09  (Deposition) - 22 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative Riboflavin Biosynthesis Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Riboflavin Biosynthesis Protein (Yp_001092907. 1) From Shewanella Sp. Pv-4 At 2. 12 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE RIBOFLAVIN BIOSYNTHESIS PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SHEW_0776
    Organism Scientific: SHEWANELLA LOIHICA
    Organism Taxid: 323850
    Strain: ATCC BAA-1088 / PV-4
    Synonym: BIFUNCTIONAL DEAMINASE-REDUCTASE DOMAIN PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 24)

Asymmetric/Biological Unit (4, 24)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION
4UNL4Ligand/IonUNKNOWN LIGAND

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:51 , ARG A:52 , ASN A:53 , THR A:54 , GLY A:115 , GLY A:116 , VAL A:117 , THR A:118 , HOH A:287BINDING SITE FOR RESIDUE SO4 A 181
2AC2SOFTWARESER A:153 , LEU A:154 , SER A:155 , ARG A:175 , HOH A:254BINDING SITE FOR RESIDUE GOL A 182
3AC3SOFTWAREMSE A:42 , PRO A:66 , TYR A:67 , SER A:68 , HOH A:250 , HOH A:281BINDING SITE FOR RESIDUE GOL A 183
4AC4SOFTWARESER A:152 , SER A:153 , LYS B:18 , ARG B:19 , HOH B:234BINDING SITE FOR RESIDUE SO4 B 181
5AC5SOFTWAREGLY B:51 , ARG B:52 , ASN B:53 , THR B:54 , GLY B:115 , GLY B:116 , VAL B:117 , THR B:118 , HOH B:198BINDING SITE FOR RESIDUE SO4 B 182
6AC6SOFTWAREPRO A:70 , PHE A:108 , HOH A:207 , HOH A:223 , ARG B:52 , SER B:75 , ASN B:76 , THR B:77 , HOH B:188BINDING SITE FOR RESIDUE SO4 B 183
7AC7SOFTWARESER B:153 , SER B:155 , ARG B:175 , LYS B:176 , ARG B:177 , HOH B:256 , HOH B:274BINDING SITE FOR RESIDUE GOL B 184
8AC8SOFTWAREASP B:126 , ILE B:128 , ASP B:129 , ARG B:175 , LYS B:176 , ARG B:177BINDING SITE FOR RESIDUE GOL B 185

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KY8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KY8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KY8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KY8)

(-) Exons   (0, 0)

(no "Exon" information available for 3KY8)

(-) 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:184
 aligned with A3QB00_SHELP | A3QB00 from UniProtKB/TrEMBL  Length:178

    Alignment length:184
                                   1                                                                                                                                                                                
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173    
         A3QB00_SHELP     - -------MANIVFIATSLDGYIADKRGKLDWLHSVPNPNNVDTGFVALMERVDGLVMGRNTLDMVLSFDCDWPYSKPVFVLSNTMTEVPQGYEDKVFLVKGKLVDIIADLNAKGFNELYIDGGVTIQNFLKEDLIDEMVITRFPILLGGGVPLFGELESSLSFNVIKSEVVLDSLTQTTYHRKR 177
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee...eee.....hhhhhhh........hhhhhhhhh.eeeeehhhhhhhh...........eeee..............eeee..hhhhhhhhhhhh...eeeeehhhhhhhhhhh....eeeeeee.ee....ee........eeeeeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ky8 A  -6 ENLYFQGmANIVFIATSLDGYIADKRGKLDWLHSVPNPNNVDTGFVALmERVDGLVmGRNTLDmVLSFDCDWPYSKPVFVLSNTmTEVPQGYEDKVFLVKGKLVDIIADLNAKGFNELYIDGGVTIQNFLKEDLIDEmVITRFPILLGGGVPLFGELESSLSFNVIKSEVVLDSLTQTTYHRKR 177
                                   | 3        13        23        33        43      | 53   |    63        73    |   83        93       103       113       123       133       143       153       163       173    
                                   1-MSE                                   42-MSE  50-MSE 57-MSE               78-MSE                                              131-MSE                                          


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with A3QB00_SHELP | A3QB00 from UniProtKB/TrEMBL  Length:178

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
         A3QB00_SHELP     1 MANIVFIATSLDGYIADKRGKLDWLHSVPNPNNVDTGFVALMERVDGLVMGRNTLDMVLSFDCDWPYSKPVFVLSNTMTEVPQGYEDKVFLVKGKLVDIIADLNAKGFNELYIDGGVTIQNFLKEDLIDEMVITRFPILLGGGVPLFGELESSLSFNVIKSEVVLDSLTQTTYHRKR 177
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --RibD_C-3ky8B01 B:3-169                                                                                                                                                 -------- Pfam domains (1)
           Pfam domains (2) --RibD_C-3ky8B02 B:3-169                                                                                                                                                 -------- Pfam domains (2)
         Sec.struct. author .eeeeeeee....eee.....hhhhhhh........hhhhhhhhh.eeeehhhhhhhhhhh.........eeee..............eeee..hhhhhhhhhhhh...eeee.hhhhhhhhhhh....eeeeee..ee....ee........eeeeeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ky8 B   1 mANIVFIATSLDGYIADKRGKLDWLHSVPNPNNVDTGFVALmERVDGLVmGRNTLDmVLSFDCDWPYSKPVFVLSNTmTEVPQGYEDKVFLVKGKLVDIIADLNAKGFNELYIDGGVTIQNFLKEDLIDEmVITRFPILLGGGVPLFGELESSLSFNVIKSEVVLDSLTQTTYHRKR 177
                            |       10        20        30        40 |      50      | 60        70       |80        90       100       110       120       130|      140       150       160       170       
                            1-MSE                                   42-MSE  50-MSE 57-MSE               78-MSE                                              131-MSE
   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 3KY8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KY8)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: DHFred (95)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A3QB00_SHELP | A3QB00)
molecular function
    GO:0008703    5-amino-6-(5-phosphoribosylamino)uracil reductase activity    Catalysis of the reaction: 5-amino-6-(5-phosphoribitylamino)uracil + NADP(+) = 5-amino-6-(5-phosphoribosylamino)uracil + H(+) + NADPH.
biological process
    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.
    GO:0009231    riboflavin biosynthetic process    The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

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