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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE DIHYDRONEOPTERIN ALDOLASE (FOLB) FROM VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. N16961
 
Authors :  B. Nocek, M. Zhou, L. Papazisi, W. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  21 Jul 10  (Deposition) - 08 Sep 10  (Release) - 08 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Biol. Unit 2:  A,B,C,D  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Clan Thbo-Biosyn (Cl0334), (Pf02152), Dihydroneopterin Aldolase, Folb, Folic Acid And Derivative Metabolic Process (Go:0006760), Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, M. Zhou, L. Papazisi, W. Anderson, A. Joachimiak
Crystal Structure Of Putative Dihydroneopterin Aldolase (Folb) From Vibrio Cholerae O1 Biovar El Tor Str. N16961
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDRONEOPTERIN ALDOLASE FOLB, PUTATIVE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD
Biological Unit 2 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:19 , GLU A:45 , ARG D:107BINDING SITE FOR RESIDUE EDO A 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O1K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O1K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O1K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O1K)

(-) Exons   (0, 0)

(no "Exon" information available for 3O1K)

(-) 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:117
 aligned with Q9KUJ6_VIBCH | Q9KUJ6 from UniProtKB/TrEMBL  Length:129

    Alignment length:117
                                    21        31        41        51        61        71        81        91       101       111       121       
         Q9KUJ6_VIBCH    12 SMDKVFIEQLEVITTIGVYDWEQQIKQKLVLDLEMAHDNRAAGKSDDVADALDYAQVSQAVLEHIEQGRFLLVERVAEEVAELIMTRFAVPWLRIRLTKPGAVPQAKGVGVIIERAR 128
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee....hhhhh.eeeeeeeeee..hhhhhhhhhhhhh.hhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3o1k A  12 SMDKVFIEQLEVITTIGVYDWEQQIKQKLVLDLEMAHDNRAAGKSDDVADALDYAQVSQAVLEHIEQGRFLLVERVAEEVAELIMTRFAVPWLRIRLTKPGAVPQAKGVGVIIERAR 128
                                    21        31        41        51        61        71        81        91       101       111       121       


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with Q9KUJ6_VIBCH | Q9KUJ6 from UniProtKB/TrEMBL  Length:129

    Alignment length:118
                                    20        30        40        50        60        70        80        90       100       110       120        
         Q9KUJ6_VIBCH    11 LSMDKVFIEQLEVITTIGVYDWEQQIKQKLVLDLEMAHDNRAAGKSDDVADALDYAQVSQAVLEHIEQGRFLLVERVAEEVAELIMTRFAVPWLRIRLTKPGAVPQAKGVGVIIERAR 128
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeee....hhhhh.eeeeeeeeee..hhhhhhhhhhhhh.hhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhhh...eeeeeeee........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3o1k B  11 LSMDKVFIEQLEVITTIGVYDWEQQIKQKLVLDLEMAHDNRAAGKSDDVADALDYAQVSQAVLEHIEQGRFLLVERVAEEVAELIMTRFAVPWLRIRLTKPGAVPQAKGVGVIIERAR 128
                                    20        30        40        50        60        70        80        90       100       110       120        


Chain C from PDB  Type:PROTEIN  Length:117
 aligned with Q9KUJ6_VIBCH | Q9KUJ6 from UniProtKB/TrEMBL  Length:129

    Alignment length:117
                                    21        31        41        51        61        71        81        91       101       111       121       
         Q9KUJ6_VIBCH    12 SMDKVFIEQLEVITTIGVYDWEQQIKQKLVLDLEMAHDNRAAGKSDDVADALDYAQVSQAVLEHIEQGRFLLVERVAEEVAELIMTRFAVPWLRIRLTKPGAVPQAKGVGVIIERAR 128
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee..hhhhhh..eeeeeeeeee..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhhhh...eeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3o1k C  12 SMDKVFIEQLEVITTIGVYDWEQQIKQKLVLDLEMAHDNRAAGKSDDVADALDYAQVSQAVLEHIEQGRFLLVERVAEEVAELIMTRFAVPWLRIRLTKPGAVPQAKGVGVIIERAR 128
                                    21        31        41        51        61        71        81        91       101       111       121       


Chain D from PDB  Type:PROTEIN  Length:118
 aligned with Q9KUJ6_VIBCH | Q9KUJ6 from UniProtKB/TrEMBL  Length:129

    Alignment length:118
                                    20        30        40        50        60        70        80        90       100       110       120        
         Q9KUJ6_VIBCH    11 LSMDKVFIEQLEVITTIGVYDWEQQIKQKLVLDLEMAHDNRAAGKSDDVADALDYAQVSQAVLEHIEQGRFLLVERVAEEVAELIMTRFAVPWLRIRLTKPGAVPQAKGVGVIIERAR 128
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----FolB-3o1kD01 D:16-126                                                                                          -- Pfam domains (1)
           Pfam domains (2) -----FolB-3o1kD02 D:16-126                                                                                          -- Pfam domains (2)
           Pfam domains (3) -----FolB-3o1kD03 D:16-126                                                                                          -- Pfam domains (3)
           Pfam domains (4) -----FolB-3o1kD04 D:16-126                                                                                          -- Pfam domains (4)
         Sec.struct. author ....eeeeeeeeeeeee..........eeeeeeeeee..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3o1k D  11 LSMDKVFIEQLEVITTIGVYDWEQQIKQKLVLDLEMAHDNRAAGKSDDVADALDYAQVSQAVLEHIEQGRFLLVERVAEEVAELIMTRFAVPWLRIRLTKPGAVPQAKGVGVIIERAR 128
                                    20        30        40        50        60        70        80        90       100       110       120
   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 3O1K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O1K)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: THBO-biosyn (64)
(-)
Family: FolB (15)
(-)
Vibrio cholerae (1)
1aFolB-3o1kD01D:16-126
1bFolB-3o1kD02D:16-126
1cFolB-3o1kD03D:16-126
1dFolB-3o1kD04D:16-126

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9KUJ6_VIBCH | Q9KUJ6)
molecular function
    GO:0004150    dihydroneopterin aldolase activity    Catalysis of the reaction: 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine = 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + glycolaldehyde.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0046656    folic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
    GO:0006760    folic acid-containing compound metabolic process    The chemical reactions and pathways involving a folic acid-containing compound, i.e. any of a group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid or L-glutamate units.
    GO:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

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2o90 RELATED ID: IDP01380 RELATED DB: TARGETDB