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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE DIHYDROFOLATE REDUCTASE (YP_805003.1) FROM PEDIOCOCCUS PENTOSACEUS ATCC 25745 AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  14 Sep 09  (Deposition) - 06 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Yp_805003. 1, Putative Dihydrofolate Reductase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Ribd C-Terminal Domain, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Dihydrofolate Reductase (Yp_805003. 1) From Pediococcus Pentosaceus Atcc 25745 At 1. 90 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    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: PEPE_1533, YP_805003.1
    Organism Scientific: PEDIOCOCCUS PENTOSACEUS ATCC 25745
    Organism Taxid: 278197
    Strain: ATCC 25745 / 183-1W

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION
4UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION
4UNL2Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION
4UNL-1Ligand/IonUNKNOWN LIGAND

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:8 , LEU A:27BINDING SITE FOR RESIDUE UNL A 178
2AC2SOFTWAREGLY A:53 , ARG A:54 , THR A:55 , THR A:56 , GLY A:117 , HOH A:271 , HOH A:289 , HOH A:295BINDING SITE FOR RESIDUE SO4 A 179
3AC3SOFTWAREARG A:54 , THR A:80 , SER A:81 , HIS A:82 , HOH A:299BINDING SITE FOR RESIDUE SO4 A 180
4AC4SOFTWAREHIS A:82 , LEU A:83 , ARG B:54 , HIS B:82BINDING SITE FOR RESIDUE EDO A 181
5AC5SOFTWAREARG B:54 , THR B:80 , SER B:81 , HOH B:1183BINDING SITE FOR RESIDUE SO4 B 178
6AC6SOFTWAREGLY B:53 , ARG B:54 , THR B:55 , THR B:56 , GLY B:117 , HOH B:1209 , HOH B:1230BINDING SITE FOR RESIDUE SO4 B 179

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:116 -Gly A:117
2Gly B:116 -Gly B:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JTW)

(-) Sequences/Alignments

Asymmetric 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:176
 aligned with Q03E11_PEDPA | Q03E11 from UniProtKB/TrEMBL  Length:177

    Alignment length:176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      
         Q03E11_PEDPA     2 ARKVILFIAMSIDNYIADDQGAVDWLEKNVHGTESDDSYEKMYSKIDTVIMGRTTYEQVTQKLSPEKYVYADRQTYIVTSHLGEDTDKIKYWKQSPVELVKRIQKEKGKDVWIVGGAKLIDPLVQANLIDTYILTTVPIFLGSGIRLFDRLEEQVPVRLIDVYQKNELVYSIYQRG 177
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...eee.....hhhhhh........hhhhhhhhheeeeeeehhhhhhhhhhh..........eeeee..........eeee..hhhhhhhhhhh....eeeeeehhhhhhhhhhh....eeeeeee.......ee..........eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jtw A   2 ARKVILFIAmSIDNYIADDQGAVDWLEKNVHGTESDDSYEKmYSKIDTVImGRTTYEQVTQKLSPEKYVYADRQTYIVTSHLGEDTDKIKYWKQSPVELVKRIQKEKGKDVWIVGGAKIIDPLVQANLIDTYILTTVPIFLGSGIRLFDRLEEQVPVRLIDVYQKNELVYSIYQRG 177
                                    11        21        31        41 |      51|       61        71        81        91       101       111       121       131       141       151       161       171      
                                    11-MSE                          43-MSE   52-MSE                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with Q03E11_PEDPA | Q03E11 from UniProtKB/TrEMBL  Length:177

    Alignment length:176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      
         Q03E11_PEDPA     2 ARKVILFIAMSIDNYIADDQGAVDWLEKNVHGTESDDSYEKMYSKIDTVIMGRTTYEQVTQKLSPEKYVYADRQTYIVTSHLGEDTDKIKYWKQSPVELVKRIQKEKGKDVWIVGGAKLIDPLVQANLIDTYILTTVPIFLGSGIRLFDRLEEQVPVRLIDVYQKNELVYSIYQRG 177
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -RibD_C-3jtwB01 B:3-170                                                                                                                                                  ------- Pfam domains (1)
           Pfam domains (2) -RibD_C-3jtwB02 B:3-170                                                                                                                                                  ------- Pfam domains (2)
         Sec.struct. author ...eeeeeeee...eee.....hhhhhhh.......hhhhhhhhheeeeeeehhhhhhhh..----.......eeeee..........eeee..hhhhhhhhhh.....eeeeeehhhhhhhhhhh....eeeeeee.......ee..........eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jtw B   2 ARKVILFIAmSIDNYIADDQGAVDWLEKNVHGTESDDSYEKmYSKIDTVImGRTTYEQVTQK----KYVYADRQTYIVTSHLGEDTDKIKYWKQSPVELVKRIQKEKGKDVWIVGGAKIIDPLVQANLIDTYILTTVPIFLGSGIRLFDRLEEQVPVRLIDVYQKNELVYSIYQRG 177
                                    11        21        31        41 |      51|       61 |    | 71        81        91       101       111       121       131       141       151       161       171      
                                    11-MSE                          43-MSE   52-MSE     63   68
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3JTW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: DHFred (95)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q03E11_PEDPA | Q03E11)
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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