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(-) Description

Title :  CRYSTAL STRUCTURE OF THE WLBA (WBPB) DEHYDROGENASE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH NAD AT 1.5 ANGSTROM RESOLUTION
 
Authors :  H. M. Holden, J. B. Thoden
Date :  04 Aug 10  (Deposition) - 18 Aug 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Sugar Biosynthesis, Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Thoden, H. M. Holden
Structural And Functional Studies Of Wlba: A Dehydrogenase Involved In The Biosynthesis Of 2, 3-Diacetamido-2, 3-Dideoxy-D-Mannuronic Acid .
Biochemistry V. 49 7939 2010
PubMed-ID: 20690587  |  Reference-DOI: 10.1021/BI101103S

(-) Compounds

Molecule 1 - WBPB
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainROSETTA2(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneWBPB
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287
    StrainPAO1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:10 , GLY A:11 , TYR A:12 , ILE A:13 , TYR A:32 , ASP A:33 , ILE A:34 , ASN A:35 , CYS A:78 , SER A:79 , PRO A:80 , ASN A:81 , LEU A:83 , HIS A:84 , HIS A:87 , GLU A:101 , LYS A:102 , PRO A:103 , GLN A:130 , TRP A:171 , LYS A:172 , ASN A:184 , HOH A:319 , HOH A:320 , HOH A:333 , HOH A:337 , HOH A:369 , HOH A:372 , HOH A:404 , GLU B:55 , HOH B:470 , SER C:37 , HOH C:391BINDING SITE FOR RESIDUE NAD A 317
2AC2SOFTWAREGLU A:55 , HOH A:560 , ALA B:10 , GLY B:11 , TYR B:12 , ILE B:13 , TYR B:32 , ASP B:33 , ILE B:34 , CYS B:78 , SER B:79 , PRO B:80 , ASN B:81 , LEU B:83 , HIS B:84 , HIS B:87 , GLU B:101 , LYS B:102 , PRO B:103 , GLN B:130 , TRP B:171 , LYS B:172 , ASN B:184 , HIS B:266 , HOH B:334 , HOH B:340 , HOH B:361 , HOH B:365 , HOH B:401 , HOH B:461 , SER D:37 , HOH D:348 , HOH D:920BINDING SITE FOR RESIDUE NAD B 317
3AC3SOFTWARESER A:37 , HOH A:446 , ALA C:10 , GLY C:11 , TYR C:12 , ILE C:13 , TYR C:32 , ASP C:33 , ILE C:34 , CYS C:78 , SER C:79 , PRO C:80 , ASN C:81 , LEU C:83 , HIS C:84 , HIS C:87 , GLU C:101 , LYS C:102 , PRO C:103 , GLN C:130 , TRP C:171 , LYS C:172 , ASN C:184 , HIS C:266 , HOH C:322 , HOH C:327 , HOH C:342 , HOH C:344 , HOH C:352 , HOH C:353 , HOH C:359 , HOH C:416 , GLU D:55BINDING SITE FOR RESIDUE NAD C 317
4AC4SOFTWARESER B:37 , HOH B:465 , GLU C:55 , HOH C:448 , ALA D:10 , GLY D:11 , TYR D:12 , ILE D:13 , TYR D:32 , ASP D:33 , ILE D:34 , ASN D:35 , CYS D:78 , SER D:79 , PRO D:80 , ASN D:81 , LEU D:83 , HIS D:84 , HIS D:87 , GLU D:101 , LYS D:102 , GLN D:130 , TRP D:171 , LYS D:172 , ASN D:184 , HOH D:318 , HOH D:321 , HOH D:329 , HOH D:330 , HOH D:345 , HOH D:616BINDING SITE FOR RESIDUE NAD D 317

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OA2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:102 -Pro A:103
2Lys B:102 -Pro B:103
3Lys C:102 -Pro C:103
4Lys D:102 -Pro D:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OA2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OA2)

(-) Exons   (0, 0)

(no "Exon" information available for 3OA2)

(-) 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:306
 aligned with WBPB_PSEAE | G3XD23 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:312
                                    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  
           WBPB_PSEAE     1 MKNFALIGAAGYIAPRHMRAIKDTGNCLVSAYDINDSVGIIDSISPQSEFFTEFEFFLDHASNLKRDSATALDYVSICSPNYLHYPHIAAGLRLGCDVICEKPLVPTPEMLDQLAVIERETDKRLYNILQLRHHQAIIALKDKVAREKSPHKYEVDLTYITSRGNWYLKSWKGDPRKSFGVATNIGVHFYDMLHFIFGKLQRNVVHFTSEYKAAGYLEYEQARVRWFLSVDANDLPESVKGKKPTYRSITVNGEEMEFSEGFTDLHTTSYEEILAGRGYGIDDARHCVETVNTIRSAVIVPASDNEGHPFVA 312
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh..eeeeee.....hhhhhhh....eee.hhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhh-....eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee...eeeeeeee..eeeeeeee.hhhhh.........eeeeeee..ee...-----hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oa2 A   1 MKNFALIGAAGYIAPRHMRAIKDTGNCLVSAYDINDSVGIIDSISPQSEFFTEFEFFLDHASNLKRDSATALDYVSICSPNYLHYPHIAAGLRLGCDVICEKPLVPTPEMLDQLAVIERETDKRLYNILQLRHHQAIIALKDKVARE-SPHKYEVDLTYITSRGNWYLKSWKGDPRKSFGVATNIGVHFYDMLHFIFGKLQRNVVHFTSEYKTAGYLEYEQARVRWFLSVDANDLPESVKGKKPTYRSITVNGEEMEF-----DLHTTSYEEILAGRGYGIDDARHCVETVNTIRSAVIVPASDNEGHPFVA 312
                                    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       | -   |   270       280       290       300       310  
                                                                                                                                                                            147 |                                                                                                          258   264                                                
                                                                                                                                                                              149                                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:311
 aligned with WBPB_PSEAE | G3XD23 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:316
                                    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      
           WBPB_PSEAE     1 MKNFALIGAAGYIAPRHMRAIKDTGNCLVSAYDINDSVGIIDSISPQSEFFTEFEFFLDHASNLKRDSATALDYVSICSPNYLHYPHIAAGLRLGCDVICEKPLVPTPEMLDQLAVIERETDKRLYNILQLRHHQAIIALKDKVAREKSPHKYEVDLTYITSRGNWYLKSWKGDPRKSFGVATNIGVHFYDMLHFIFGKLQRNVVHFTSEYKAAGYLEYEQARVRWFLSVDANDLPESVKGKKPTYRSITVNGEEMEFSEGFTDLHTTSYEEILAGRGYGIDDARHCVETVNTIRSAVIVPASDNEGHPFVAALAR 316
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh..eeeeee.....hhhhhhh....eee.hhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh....eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee...eeeeeeee..eeeeeeee.hhhhh.........eeeeeee..ee...-----hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oa2 B   1 MKNFALIGAAGYIAPRHMRAIKDTGNCLVSAYDINDSVGIIDSISPQSEFFTEFEFFLDHASNLKRDSATALDYVSICSPNYLHYPHIAAGLRLGCDVICEKPLVPTPEMLDQLAVIERETDKRLYNILQLRHHQAIIALKDKVAREKSPHKYEVDLTYITSRGNWYLKSWKGDPRKSFGVATNIGVHFYDMLHFIFGKLQRNVVHFTSEYKTAGYLEYEQARVRWFLSVDANDLPESVKGKKPTYRSITVNGEEMEF-----DLHTTSYEEILAGRGYGIDDARHCVETVNTIRSAVIVPASDNEGHPFVAALAR 316
                                    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       | -   |   270       280       290       300       310      
                                                                                                                                                                                                                                                                                           258   264                                                    

Chain C from PDB  Type:PROTEIN  Length:299
 aligned with WBPB_PSEAE | G3XD23 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:311
                                    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 
           WBPB_PSEAE     1 MKNFALIGAAGYIAPRHMRAIKDTGNCLVSAYDINDSVGIIDSISPQSEFFTEFEFFLDHASNLKRDSATALDYVSICSPNYLHYPHIAAGLRLGCDVICEKPLVPTPEMLDQLAVIERETDKRLYNILQLRHHQAIIALKDKVAREKSPHKYEVDLTYITSRGNWYLKSWKGDPRKSFGVATNIGVHFYDMLHFIFGKLQRNVVHFTSEYKAAGYLEYEQARVRWFLSVDANDLPESVKGKKPTYRSITVNGEEMEFSEGFTDLHTTSYEEILAGRGYGIDDARHCVETVNTIRSAVIVPASDNEGHPFV 311
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh..eeeeee.....hhhhhhh....eee.hhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhh.....eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee...eeeeeeee..eeeeeeee.hhhhh.-------.eeeeeee..ee...-----hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oa2 C   1 MKNFALIGAAGYIAPRHMRAIKDTGNCLVSAYDINDSVGIIDSISPQSEFFTEFEFFLDHASNLKRDSATALDYVSICSPNYLHYPHIAAGLRLGCDVICEKPLVPTPEMLDQLAVIERETDKRLYNILQLRHHQAIIALKDKVAREKSPHKYEVDLTYITSRGNWYLKSWKGDPRKSFGVATNIGVHFYDMLHFIFGKLQRNVVHFTSEYKTAGYLEYEQARVRWFLSVDANDLP-------PTYRSITVNGEEMEF-----DLHTTSYEEILAGRGYGIDDARHCVETVNTIRSAVIVPASDNEGHPFV 311
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     |   -   |   250       | -   |   270       280       290       300       310 
                                                                                                                                                                                                                                                                     236     244           258   264                                               

Chain D from PDB  Type:PROTEIN  Length:298
 aligned with WBPB_PSEAE | G3XD23 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:311
                                    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 
           WBPB_PSEAE     1 MKNFALIGAAGYIAPRHMRAIKDTGNCLVSAYDINDSVGIIDSISPQSEFFTEFEFFLDHASNLKRDSATALDYVSICSPNYLHYPHIAAGLRLGCDVICEKPLVPTPEMLDQLAVIERETDKRLYNILQLRHHQAIIALKDKVAREKSPHKYEVDLTYITSRGNWYLKSWKGDPRKSFGVATNIGVHFYDMLHFIFGKLQRNVVHFTSEYKAAGYLEYEQARVRWFLSVDANDLPESVKGKKPTYRSITVNGEEMEFSEGFTDLHTTSYEEILAGRGYGIDDARHCVETVNTIRSAVIVPASDNEGHPFV 311
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh..eeeeee.....hhhhhhh....eee.hhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh------.eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee...eeeeeeee..eeeeeeee.hhhhh.........eeeeeee..ee.-------hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oa2 D   1 MKNFALIGAAGYIAPRHMRAIKDTGNCLVSAYDINDSVGIIDSISPQSEFFTEFEFFLDHASNLKRDSATALDYVSICSPNYLHYPHIAAGLRLGCDVICEKPLVPTPEMLDQLAVIERETDKRLYNILQLRHHQAIIALKDKVA------KYEVDLTYITSRGNWYLKSWKGDPRKSFGVATNIGVHFYDMLHFIFGKLQRNVVHFTSEYKTAGYLEYEQARVRWFLSVDANDLPESVKGKKPTYRSITVNGEEM-------DLHTTSYEEILAGRGYGIDDARHCVETVNTIRSAVIVPASDNEGHPFV 311
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    |    - |     160       170       180       190       200       210       220       230       240       250     |   -   |   270       280       290       300       310 
                                                                                                                                                                          145    152                                                                                                     256     264                                               

   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 3OA2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OA2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OA2)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (WBPB_PSEAE | G3XD23)
molecular function
    GO:0070404    NADH binding    Interacting selectively and non-covalently with the reduced form, NADH, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0009243    O antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.

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 Related Entries

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(-) Related Entries Specified in the PDB File

3o9z HOMOLOGUE FROM THERMUS THERMOPHILUS IN COMPLEX WITH NAD AND ALPHA-KETOGLUTARATE
3oa0 HOMOLOGUE FROM THERMUS THERMOPHILUS IN COMPLEX WITH NAD AND UDP-GLCNACA