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(-) Description

Title :  NATIVE STRUCTURE OF THE UDP-N-ACETYL-MANNOSAMINE DEHYDROGENASE CAP5O FROM STAPHYLOCOCCUS AUREUS
 
Authors :  S. Nessler, J. Gruszczyk, V. Olivares-Illana, P. Meyer, S. Morera, C. Grangeasse, A. Fleurie
Date :  23 Aug 10  (Deposition) - 23 Mar 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Binary Complex, Cofactor Nad, Dimer, Oxidoreduction, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Gruszczyk, A. Fleurie, V. Olivares-Illana, E. Bechet, I. Zanella-Cleon, S. Morera, P. Meyer, G. Pompidor, R. Kahn, C. Grangeasse, S. Nessler
Structure Analysis Of The Staphylococcus Aureus Udp-N-Acetyl-Mannosamine Dehydrogenase Cap5O Involved In Capsular Polysaccharide Biosynthesis.
J. Biol. Chem. V. 286 17112 2011
PubMed-ID: 21454499  |  Reference-DOI: 10.1074/JBC.M110.216002

(-) Compounds

Molecule 1 - CAP5O
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CAP5O
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: REYNOLDS AND NEWMAN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:6 , GLY A:7 , GLY A:9 , TYR A:10 , ILE A:11 , ASP A:30 , ILE A:31 , VAL A:80 , PRO A:81 , THR A:82 , LEU A:96 , ARG A:99 , THR A:119 , VAL A:153 , CYS A:258 , ASP B:351BINDING SITE FOR RESIDUE NAD A 500
2AC2SOFTWAREASN A:135 , VAL B:6 , GLY B:7 , GLY B:9 , TYR B:10 , ILE B:11 , ASP B:30 , ILE B:31 , VAL B:80 , PRO B:81 , THR B:82 , LEU B:96 , ARG B:99 , THR B:119 , GLU B:151 , VAL B:153 , ARG B:322 , HOH B:425 , HOH B:428BINDING SITE FOR RESIDUE NAD B 500

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:92 -B:258

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OJL)

(-) 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:418
 aligned with P95708_STAAU | P95708 from UniProtKB/TrEMBL  Length:420

    Alignment length:418
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410        
         P95708_STAAU     1 MKLTVVGLGYIGLPTSIMFAKHGVDVLGVDINQQTIDKLQNGQISIEEPGLQEVYEEVLSSGKLKVSTTPEASDVFIIAVPTPNNDDQYRSCDISLVMRALDSILPFLKKGNTIIVESTIAPKTMDDFVKPVIENLGFTIGEDIYLVHCPERVLPGKILEELVHNNRIIGGVTKACIEAGKRVYRTFVQGEMIETDARTAEMSKLMENTYRDVNIALANELTKICNNLNINVLDVIEMANKHPRVNIHQPGPGVGGHCLAVDPYFIIAKDPENAKLIQTGREINNSMPAYVVDTTKQIIKALSGNKVTVFGLTYKGDVDDIRESPAFDIYELLNQEPDIEVCAYDPHVELDFVEHDMSHAVKDASLVLILSDHSEFKNLSDSHFDKMKHKVIFDTKNVVKSSFEDVLYYNYGNIFNFI 418
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhh........hhhhhhhhhhhh..eeee.......eeee...............hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh.........eeee........hhhhhhhhh.eeeee.hhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhh...eee.............hhhhhhh....eee...hhhhh.............eeee............eee...hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ojl A   1 SKLTVVGLGYIGLPTSIMFAKHGVDVLGVDINQQTIDKLQNGQISIEEPGLQEVYEEVLSSGKLKVSTTPEASDVFIIAVPTPNNDDQYRSCDISLVMRALDSILPFLKKGNTIIVESTIAPKTMDDFVKPVIENLGFTIGEDIYLVHCPERVLPGKILEELVHNNRIIGGVTKACIEAGKRVYRTFVQGEMIETDARTAEMSKLMENTYRDVNIALANELTKICNNLNINVLDVIEMANKHPRVNIHQPGPGVGGHCLAVDPYFIIAKDPENAKLIQTGREINNSMPAYVVDTTKQIIKALSGNKVTVFGLTYKGDVDDIRESPAFDIYELLNQEPDIEVCAYDPHVELDFVEHDMSHAVKDASLVLILSDHSEFKNLSDSHFDKMKHKVIFDTKNVVKSSFEDVLYYNYGNIFNFI 418
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410        


Chain B from PDB  Type:PROTEIN  Length:412
 aligned with P95708_STAAU | P95708 from UniProtKB/TrEMBL  Length:420

    Alignment length:419
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410         
         P95708_STAAU     1 MKLTVVGLGYIGLPTSIMFAKHGVDVLGVDINQQTIDKLQNGQISIEEPGLQEVYEEVLSSGKLKVSTTPEASDVFIIAVPTPNNDDQYRSCDISLVMRALDSILPFLKKGNTIIVESTIAPKTMDDFVKPVIENLGFTIGEDIYLVHCPERVLPGKILEELVHNNRIIGGVTKACIEAGKRVYRTFVQGEMIETDARTAEMSKLMENTYRDVNIALANELTKICNNLNINVLDVIEMANKHPRVNIHQPGPGVGGHCLAVDPYFIIAKDPENAKLIQTGREINNSMPAYVVDTTKQIIKALSGNKVTVFGLTYKGDVDDIRESPAFDIYELLNQEPDIEVCAYDPHVELDFVEHDMSHAVKDASLVLILSDHSEFKNLSDSHFDKMKHKVIFDTKNVVKSSFEDVLYYNYGNIFNFID 419
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -UDPG_MGDP_dh_N-3ojlB03 B:2-185                                                                                                                                                          -----------UDPG_MGDP_dh-3ojlB01 B:197-289                                                               ------------------UDPG_MGDP_dh_C-3ojlB05 B:308-401                                                              ------------------ Pfam domains (1)
           Pfam domains (2) -UDPG_MGDP_dh_N-3ojlB04 B:2-185                                                                                                                                                          -----------UDPG_MGDP_dh-3ojlB02 B:197-289                                                               ------------------UDPG_MGDP_dh_C-3ojlB06 B:308-401                                                              ------------------ Pfam domains (2)
         Sec.struct. author .eeeee....hhhhhhhhhhh...eeeee..hhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.......eeee.....ee.....ee.hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh.........eeee........hhhhhhhhh.eeeee.hhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.........................-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhh...eeeee........ee.hhhhhhh...eeee...hhhhh.............eeee............eee...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ojl B   1 SKLTVVGLGYIGLPTSIMFAKHGVDVLGVDINQQTIDKLQNGQISIEEPGLQEVYEEVLSSGKLKVSTTPEASDVFIIAVPTPNNDDQYRSCDISLVMRALDSILPFLKKGNTIIVESTIAPKTMDDFVKPVIENLGFTIGEDIYLVHCPERVLPGKILEELVHNNRIIGGVTKACIEAGKRVYRTFVQGEMIETDARTAEMSKLMENTYRDVNIALANELTKICNNLNINVLDVIEMANKHPRVNIHQPGPGVGGHCLAVDPYF-------NAKLIQTGREINNSMPAYVVDTTKQIIKALSGNKVTVFGLTYKGDVDDIRESPAFDIYELLNQEPDIEVCAYDPHVELDFVEHDMSHAVKDASLVLILSDHSEFKNLSDSHFDKMKHKVIFDTKNVVKSSFEDVLYYNYGNIFNFID 419
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    |    -  |    280       290       300       310       320       330       340       350       360       370       380       390       400       410         
                                                                                                                                                                                                                                                                                                  265     273
   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 3OJL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: 6PGD_C (47)
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: UDPG_MGDP_dh_C] (10)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P95708_STAAU | P95708)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    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:0016628    oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
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:0000271    polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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 Related Entries

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UniProtKB/TrEMBL
        P95708_STAAU | P95708: 3ojo

(-) Related Entries Specified in the PDB File

3ojo DERIVATIVE STRUCTURE OF THE UDP-N-ACETYL-MANNOSAMINE DEHYDROGENASE CAP5O FROM STAPHYLOCOCCUS AUREUS