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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE DIHYDROFOLATE REDUCTASE (BSU40760, YYAP) FROM BACILLUS SUBTILIS AT 2.30 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  15 Mar 06  (Deposition) - 28 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  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 (2636623) From Bacillus Subtilis At 2. 30 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YYAP
    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: YYAP
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:53 , LYS A:55 , SER A:56 , ARG A:90 , GLY A:126BINDING SITE FOR RESIDUE CL A 189
2AC2SOFTWARELYS A:55 , ARG A:90 , SER A:128 , LYS A:155 , EDO A:192 , HOH A:200 , HOH A:265 , HOH A:268BINDING SITE FOR RESIDUE PO4 A 190
3AC3SOFTWARELYS B:55 , ALA B:127 , SER B:128 , LYS B:155 , HOH B:228 , HOH B:251BINDING SITE FOR RESIDUE PO4 B 189
4AC4SOFTWAREILE A:22 , GLU A:23 , ILE A:130 , HOH A:229 , HOH A:276BINDING SITE FOR RESIDUE EDO A 191
5AC5SOFTWARELYS A:155 , PO4 A:190 , HOH A:256BINDING SITE FOR RESIDUE EDO A 192
6AC6SOFTWARELEU B:14 , GLU B:23 , TYR B:124 , ALA B:127 , HOH B:252BINDING SITE FOR RESIDUE EDO B 190
7AC7SOFTWARETHR A:17 , LEU A:18 , THR B:17 , LEU B:18BINDING SITE FOR RESIDUE EDO A 193

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GD9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:125 -Gly A:126
2Gly B:125 -Gly B:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GD9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GD9)

(-) Exons   (0, 0)

(no "Exon" information available for 2GD9)

(-) 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:177
 aligned with YYAP_BACSU | P37508 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:187
                             1                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       
           YYAP_BACSU     - -MTNNLKQRRIILDLAVTLDGFIEGKNGEVDWCIMDPDMGFTDFLNQIDTILYGRKSFDLWGQYIPKNEDPDTEKELWKLVHSKKKYVFSRTQNEIDNQAIFINDNILEEVNKLKKNPGKDIWLYGGASLITTFINLGLVDEFRLSIHPVVLGEGKPLFIDVKQRINLKMVNTRTFSSGVVQIVYHW 186
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeee....eee...............hhhhhhhheeeeeeehhhhhhhh..----------.hhhhhhhhheeeee..eee....eee.hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhh....eeeeee..ee....ee........ee.eeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gd9 A   0 GmTNNLKQRRIILDLAVTLDGFIEGKNGEVDWCImDPDmGFTDFLNQIDTILYGRKSFDLWGQY----------KELWKLVHSKKKYVFSRTQNEIDNQAIFINDNILEEVNKLKKNPGKDIWLYGGASLITTFINLGLVDEFRLSIHPVVLGEGKPLFIDVKQRINLKmVNTRTFSSGVVQIVYHW 186
                             |       9        19        29    |   39        49        59   |     -    |   79        89        99       109       119       129       139       149       159       169       179       
                             |                               34-MSE                       63         74                                                                                            169-MSE             
                             1-MSE                               38-MSE                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:171
 aligned with YYAP_BACSU | P37508 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:188
                             1                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179        
           YYAP_BACSU     - -MTNNLKQRRIILDLAVTLDGFIEGKNGEVDWCIMDPDMGFTDFLNQIDTILYGRKSFDLWGQYIPKNEDPDTEKELWKLVHSKKKYVFSRTQNEIDNQAIFINDNILEEVNKLKKNPGKDIWLYGGASLITTFINLGLVDEFRLSIHPVVLGEGKPLFIDVKQRINLKMVNTRTFSSGVVQIVYHWN 187
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee...eee...........hhhhhhhhhhhheeeeeeehhhhhhhh...--------hhhhhhhhhh.eeeee..---------..hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh....eeeeeee.ee....ee........ee.eeeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gd9 B   0 GmTNNLKQRRIILDLAVTLDGFIEGKNGEVDWCImDPDmGFTDFLNQIDTILYGRKSFDLWGQYI--------EKELWKLVHSKKKYVFSR---------IFINDNILEEVNKLKKNPGKDIWLYGGASLITTFINLGLVDEFRLSIHPVVLGEGKPLFIDVKQRINLKmVNTRTFSSGVVQIVYHWN 187
                             |       9        19        29    |   39        49        59    |    -   |    79        89|        -|      109       119       129       139       149       159       169       179        
                             1-MSE                           34-MSE                        64       73               90       100                                                                  169-MSE              
                                                                 38-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 2GD9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GD9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GD9)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YYAP_BACSU | P37508)
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:0019239    deaminase activity    Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
    GO:0009982    pseudouridine synthase activity    Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
biological process
    GO:0000455    enzyme-directed rRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine during ribosome biogenesis where the enzyme specifies the site that becomes pseudouridylated without using a guide RNA.
    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).
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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