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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE DIHYDROFOLATE REDUCTASE (YP_001636057.1) FROM CHLOROFLEXUS AURANTIACUS J-10-FL AT 1.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  29 Oct 09  (Deposition) - 24 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative Dihydrofolate Reductase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Dihydrofolate Reductase (Yp_001636057. 1) From Chloroflexus Aurantiacus J-10-Fl At 1. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BIFUNCTIONAL DEAMINASE-REDUCTASE DOMAIN 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: CAUR_2460
    Organism Scientific: CHLOROFLEXUS AURANTIACUS J-10-FL
    Organism Taxid: 324602
    Strain: ATCC 29366 / DSM 635 / J-10-FL

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 38)

Asymmetric/Biological Unit (4, 38)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO18Ligand/Ion1,2-ETHANEDIOL
3MSE16Mod. Amino AcidSELENOMETHIONINE
4NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:8 , SER A:9 , MSE A:16 , ALA A:17 , MSE A:21 , TRP A:38 , LEU A:41 , MSE A:42 , GLY A:83 , LYS A:84 , ARG A:85 , MSE A:86 , LEU A:107 , THR A:108 , HIS A:109 , PRO A:130 , SER A:149 , GLY A:151 , ALA A:152 , ASN A:153 , VAL A:154 , GLN A:157 , ARG A:180 , EDO A:215 , HOH A:229 , HOH A:255 , HOH A:261 , HOH A:263 , HOH A:282 , HOH A:322 , HOH A:346 , HOH A:357 , HOH A:360 , HOH A:366 , HOH A:408 , HOH A:416 , HOH B:315BINDING SITE FOR RESIDUE NDP A 301
02AC2SOFTWAREASN A:153 , GLN A:156 , GLN A:157 , ASN A:160 , ASN A:185 , HOH A:385BINDING SITE FOR RESIDUE EDO A 213
03AC3SOFTWARETHR A:122 , TYR A:124 , ASN A:160 , LEU A:161 , HIS A:187BINDING SITE FOR RESIDUE EDO A 214
04AC4SOFTWAREMSE A:21 , ARG A:85 , GLY A:89 , HOH A:294 , NDP A:301BINDING SITE FOR RESIDUE EDO A 215
05AC5SOFTWAREVAL A:116 , PRO A:118 , LEU A:161BINDING SITE FOR RESIDUE EDO A 216
06AC6SOFTWAREVAL A:116 , PRO A:189 , HOH A:291 , HOH A:317BINDING SITE FOR RESIDUE EDO A 217
07AC7SOFTWAREASN A:33 , ALA A:36 , VAL A:174BINDING SITE FOR RESIDUE EDO A 218
08AC8SOFTWAREHOH A:290 , HOH A:321 , ILE B:8 , SER B:9 , MSE B:16 , ALA B:17 , MSE B:21 , TRP B:38 , LEU B:41 , MSE B:42 , GLY B:83 , LYS B:84 , ARG B:85 , MSE B:86 , LEU B:107 , THR B:108 , HIS B:109 , PRO B:130 , SER B:149 , GLY B:151 , ALA B:152 , ASN B:153 , VAL B:154 , GLN B:157 , ARG B:180 , CL B:214 , EDO B:222 , HOH B:242 , HOH B:253 , HOH B:307 , HOH B:308 , HOH B:319 , HOH B:320 , HOH B:329 , HOH B:337 , HOH B:338 , HOH B:379 , HOH B:424BINDING SITE FOR RESIDUE NDP B 301
09AC9SOFTWAREVAL B:126 , ASN B:127 , ASP B:128 , HOH B:322 , HOH B:464BINDING SITE FOR RESIDUE CL B 213
10BC1SOFTWARETHR A:63 , HOH A:411 , LYS B:84 , NDP B:301BINDING SITE FOR RESIDUE CL B 214
11BC2SOFTWARELEU A:12 , LEU B:12 , HOH B:254 , HOH B:255BINDING SITE FOR RESIDUE EDO B 215
12BC3SOFTWARELEU A:186 , HOH A:526 , PHE B:176 , GLY B:177BINDING SITE FOR RESIDUE EDO B 216
13BC4SOFTWARETHR B:122 , TYR B:124 , ASN B:160 , LEU B:161 , HIS B:187 , EDO B:219 , HOH B:324 , HOH B:348 , HOH B:499BINDING SITE FOR RESIDUE EDO B 217
14BC5SOFTWAREVAL B:116 , PRO B:118 , GLU B:131 , LEU B:161BINDING SITE FOR RESIDUE EDO B 218
15BC6SOFTWAREASN B:153 , GLN B:156 , GLN B:157 , ASN B:160 , EDO B:217 , EDO B:222 , HOH B:418 , HOH B:499BINDING SITE FOR RESIDUE EDO B 219
16BC7SOFTWAREGLU A:62 , HOH A:290 , HIS B:109 , GLU B:110 , GLU B:143BINDING SITE FOR RESIDUE EDO B 220
17BC8SOFTWAREASN B:7 , SER B:9 , ARG B:147 , HOH B:242 , HOH B:397 , HOH B:524BINDING SITE FOR RESIDUE EDO B 221
18BC9SOFTWAREASN B:153 , GLN B:157 , EDO B:219 , HOH B:267 , NDP B:301BINDING SITE FOR RESIDUE EDO B 222
19CC1SOFTWAREVAL B:116 , ASN B:160 , LEU B:161 , GLY B:162 , PRO B:189 , HOH B:296 , HOH B:364 , HOH B:381BINDING SITE FOR RESIDUE EDO B 223
20CC2SOFTWARETHR B:59 , GLY B:60BINDING SITE FOR RESIDUE EDO B 224
21CC3SOFTWAREPRO B:103 , TYR B:124 , HOH B:244 , HOH B:348 , HOH B:367 , HOH B:478 , HOH B:499BINDING SITE FOR RESIDUE EDO B 225
22CC4SOFTWAREGLN A:192 , ALA B:36 , HOH B:462 , HOH B:547BINDING SITE FOR RESIDUE EDO B 226

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:150 -Gly A:151
2Glu A:188 -Pro A:189
3Gly B:150 -Gly B:151
4Glu B:188 -Pro B:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KGY)

(-) 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:218
 aligned with A9WHX7_CHLAA | A9WHX7 from UniProtKB/TrEMBL  Length:212

    Alignment length:218
                                  1                                                                                                                                                                                                                   
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204        
         A9WHX7_CHLAA     - ------MSKVFVNISLSLDGFMAPEGMDMAHFSDPTYKNWGAKWGALMAWALSQQYLREKLKLGTGGETGPVNDMVRHTFERTGAHIMGKRMFEGGERGWPEEAPFHTPVYVLTHERRNPWVRPGGTTFYFVNDGPEQALALAREAAGERDIRISGGANVIQQYLNLGLVDELEIALIPVIFGGGRRLFENLHEPLPQFRIDRVLASPTATHLRYVRL 212
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..eeeeeeee...eee....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhheeeeeeehhhhhhhhhhh........eeeee.......eee...eeeeee..hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh....eeeeeee.......ee...........eeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kgy A  -5 NLYFQGmSKVFVNISLSLDGFmAPEGmDmAHFSDPTYKNWGAKWGALmAWALSQQYLREKLKLGTGGETGPVNDmVRHTFERTGAHImGKRmFEGGERGWPEEAPFHTPVYVLTHERRNPWVRPGGTTFYFVNDGPEQALALAREAAGERDIRISGGANVIQQYLNLGLVDELEIALIPVIFGGGRRLFENLHEPLPQFRIDRVLASPTATHLRYVRL 212
                                  |  4        14 |    | 24        34       |44        54        64    |   74       |84 |      94       104       114       124       134       144       154       164       174       184       194       204        
                                  1-MSE         16-MSE| |                 42-MSE                     69-MSE       82-MSE                                                                                                                              
                                                     21-MSE                                                           86-MSE                                                                                                                          
                                                       23-MSE                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with A9WHX7_CHLAA | A9WHX7 from UniProtKB/TrEMBL  Length:212

    Alignment length:218
                                  1                                                                                                                                                                                                                   
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204        
         A9WHX7_CHLAA     - ------MSKVFVNISLSLDGFMAPEGMDMAHFSDPTYKNWGAKWGALMAWALSQQYLREKLKLGTGGETGPVNDMVRHTFERTGAHIMGKRMFEGGERGWPEEAPFHTPVYVLTHERRNPWVRPGGTTFYFVNDGPEQALALAREAAGERDIRISGGANVIQQYLNLGLVDELEIALIPVIFGGGRRLFENLHEPLPQFRIDRVLASPTATHLRYVRL 212
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------RibD_C-3kgyB01 B:2-207                                                                                                                                                                                        ----- Pfam domains (1)
           Pfam domains (2) -------RibD_C-3kgyB02 B:2-207                                                                                                                                                                                        ----- Pfam domains (2)
         Sec.struct. author ..hhhhh..eeeeeeee..........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhheeeeeeehhhhhhhhhhh........eeeee.......eee...eeeeee..hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh....eeeeeee....................eeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kgy B  -5 NLYFQGmSKVFVNISLSLDGFmAPEGmDmAHFSDPTYKNWGAKWGALmAWALSQQYLREKLKLGTGGETGPVNDmVRHTFERTGAHImGKRmFEGGERGWPEEAPFHTPVYVLTHERRNPWVRPGGTTFYFVNDGPEQALALAREAAGERDIRISGGANVIQQYLNLGLVDELEIALIPVIFGGGRRLFENLHEPLPQFRIDRVLASPTATHLRYVRL 212
                                  |  4        14 |    | 24        34       |44        54        64    |   74       |84 |      94       104       114       124       134       144       154       164       174       184       194       204        
                                  1-MSE         16-MSE| |                 42-MSE                     69-MSE       82-MSE                                                                                                                              
                                                     21-MSE                                                           86-MSE                                                                                                                          
                                                       23-MSE
   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 3KGY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A9WHX7_CHLAA | A9WHX7)
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.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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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