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(-) Description

Title :  CRYSTAL STRUCTURE OF BIFUNCTIONAL FOLYLPOLYGLUTAMATE SYNTHASE/DIHYDROFOLATE SYNTHASE WITH MN, AMPPNP AND L-GLUTAMATE BOUND
 
Authors :  B. Nocek, M. Makowska-Grzyska, N. Maltseva, W. Anderson, A. Joachimia For Structural Genomics Of Infectious Diseases (Csgid)
Date :  17 Jan 11  (Deposition) - 02 Feb 11  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Csgid, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Folc, Dihydrofolate Synthetase- Folylpolyglutamate Synthetase, Dhfs, Amppnp, Mn, L-Glu, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, M. Makowska-Grzyska, N. Maltseva, W. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Bifunctional Folylpolyglutamate Synthase/Dihydrofolate Synthase With Mn, Amppnp And L-Glutamate Bound
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDROFOLATE SYNTHASE / FOLYLPOLYGLUTAMATE SYNTHASE
    Chains: A
    EC Number: 6.3.2.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PMCSG7
    Gene: DEDC, YPO2769
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GOL2Ligand/IonGLYCEROL
4MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:57 , ASN A:58 , GLY A:59 , LYS A:60 , GLY A:61 , THR A:62 , SER A:83 , PRO A:84 , GLU A:146 , ASN A:269 , ARG A:301 , ASP A:314 , VAL A:315 , ALA A:316 , HIS A:317 , HIS A:320 , ALA A:321 , TYR A:324 , PHE A:422 , HOH A:436 , HOH A:437 , HOH A:458 , HOH A:531 , HOH A:596 , MN A:601BINDING SITE FOR RESIDUE ANP A 501
2AC2SOFTWARESER A:83 , GLU A:146 , HOH A:436 , HOH A:437 , ANP A:501BINDING SITE FOR RESIDUE MN A 601
3AC3SOFTWARETYR A:179 , ARG A:255 , GLN A:256BINDING SITE FOR RESIDUE GOL A 435
4AC4SOFTWAREARG A:323BINDING SITE FOR RESIDUE GOL A 602
5AC5SOFTWARETHR A:57 , LEU A:149 , GLY A:150 , ALA A:170 , LEU A:171 , ASP A:172 , HIS A:173 , TYR A:179 , LYS A:188 , HOH A:465BINDING SITE FOR RESIDUE GLU A 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:83 -Pro A:84
2Gln A:308 -Pro A:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QCZ)

(-) 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:407
 aligned with Q0WDC2_YERPE | Q0WDC2 from UniProtKB/TrEMBL  Length:434

    Alignment length:431
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       434 
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434 
         Q0WDC2_YERPE     5 QTPQATSPLAAWLCYLEHLHSQPIELGLERVKQVAERLDLLKPAPKIFTVAGTNGKGTTCCTLEAILLAAGLRVGVYSSPHLLRYTERVRIQGQELSEAEHSHSFAQIEAGRGDISLTYFEFGTLSALQLFKQAKLDVVILEVGLGGRLDATNIVDSDVAAITSIALDHTDWLGYDRESIGREKAGVFRGGKPAVVGEPDMPQSIADVAAELGAQLYRRDVAWKFSQQEPFDQQEPVDQQINGWHWQCGERQLTGLPVPNVPLANAATALAVLHYSELPLSDEAIRQGLQAASLPGRFQVVSEQPLLILDVAHNPHAARYLVNRLAQVINPVNASKQGKVRAVVGMLSDKDIAGTLACLSERVDEWYCAPLEGPRGASAGQLAEHLVSARQFSDVETAWRQAMQDADTQDVVIVCGSFHTVAHVMAALHL-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------   -------------------------Mur_ligase_M-3qczA02 A:54-277                                                                                                                                                                                                   --------------------Mur_ligase_C-3qczA01 A:298-384                                                         --------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh...---...hhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhhh...eeee......hhhh.eee..ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eeeee.......hhhhhh...eeee.............hhhhhhhhhhh......eeee.....hhhhhhhhhhhh.eeee....eeee.--------------..eeeee..eeeeee.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh......eeee...eeee....hhhhhhhhhhhhhh..-------...eeeee......hhhhhhhhhh....eeee.........hhhhhhh.....ee..hhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qcz A   5 QTPQATSPLAAWLCYLEHLHS---ELGLERVKQVAERLDLLKPAPKIFTVAGTNGKGTTCCTLEAILLAAGLRVGVYSSPHLLRYTERVRIQGQELSEAEHSHSFAQIEAGRGDISLTYFEFGTLSALQLFKQAKLDVVILEVGLGGRLDATNIVDSDVAAITSIALDHTDWLGYDRESIGREKAGVFRGGKPAVVGEPDMPQSIADVAAELGAQLYRRDVAWKFSQ--------------NGWHWQCGERQLTGLPVPNVPLANAATALAVLHYSELPLSDEAIRQGLQAASLPGRFQVVSEQPLLILDVAHNPHAARYLVNRLAQVI-------QGKVRAVVGMLSDKDIAGTLACLSERVDEWYCAPLEGPRGASAGQLAEHLVSARQFSDVETAWRQAMQDADTQDVVIVCGSFHTVAHVMAALHLE 701
                                    14        24|   |   34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224      |  -         - |     254       264       274       284       294       304       314       324        |-      |344       354       364       374       384       394       404       414       424       434|
                                               25  29                                                                                                                                                                                                       231            246                                                                                    333     341                                                                                          434|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        701
   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 3QCZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Mur_ligase_C] (24)
(-)
Clan: no clan defined [family: Mur_ligase_M] (23)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q0WDC2_YERPE | Q0WDC2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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.
    GO:0004326    tetrahydrofolylpolyglutamate synthase activity    Catalysis of the reaction: ATP + tetrahydrofolyl-(Glu)(n) + L-glutamate = ADP + phosphate + tetrahydrofolyl-(Glu)(n+1).
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0009396    folic acid-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
    GO:0046901    tetrahydrofolylpolyglutamate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolylpolyglutamate, a folate derivative comprising tetrahydrofolate attached to a chain of glutamate residues.

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3n2a RELATED ID: IDP90784 RELATED DB: TARGETDB