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(-) Description

Title :  CRYSTAL STRUCTURE OF THE WLBA DEHYDROGNASE FROM CHROMOBACTRIUM VIOLACEUM IN COMPLEX WITH NADH AND UDP-GLCNACA AT 1.50 A RESOLUTION
 
Authors :  H. M. Holden, J. B. Thoden
Date :  20 Dec 10  (Deposition) - 19 Jan 11  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Rossmann Fold, Dehydrogenase, Udp-Sugar Binding, Nad Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Thoden, H. M. Holden
Biochemical And Structural Characterization Of Wlba From Bordetella Pertussis And Chromobacterium Violaceum: Enzymes Required For The Biosynthesis Of 2, 3-Diacetamido-2, 3-Dideoxy-D-Mannuronic Acid.
Biochemistry V. 50 1483 2011
PubMed-ID: 21241053  |  Reference-DOI: 10.1021/BI101871F

(-) Compounds

Molecule 1 - DEHYDROGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CV_4127, WLBA
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536
    Synonym: WLBA DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (8x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2HP71Ligand/Ion(2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[(2R,3S,4R,5R)-5-(2,4-DIOXOPYRIMIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXY-3,4-DIHYDROXY-OXANE-2-CARBOXYLIC ACID
3NA1Ligand/IonSODIUM ION
4NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HP78Ligand/Ion(2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[(2R,3S,4R,5R)-5-(2,4-DIOXOPYRIMIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXY-3,4-DIHYDROXY-OXANE-2-CARBOXYLIC ACID
3NA-1Ligand/IonSODIUM ION
4NAI8Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:17 , GLY A:18 , CYS A:19 , GLY A:20 , ARG A:21 , ILE A:22 , ASP A:44 , ILE A:45 , LYS A:51 , THR A:80 , THR A:81 , PRO A:82 , SER A:83 , LEU A:85 , HIS A:86 , GLN A:89 , GLU A:103 , LYS A:104 , GLN A:132 , TRP A:175 , ARG A:176 , HIS A:192 , HOH A:360 , HOH A:423 , HOH A:490 , HOH A:520 , HOH A:527 , HOH A:581 , HOH A:582 , HOH A:584BINDING SITE FOR RESIDUE NAI A 500
2AC2SOFTWARELYS A:104 , ASN A:133 , TRP A:163 , THR A:164 , ARG A:165 , PRO A:166 , TYR A:169 , ASN A:188 , GLN A:189 , HIS A:192 , LYS A:247 , ASN A:248 , HOH A:395 , HOH A:424 , HOH A:444 , HOH A:446 , HOH A:481 , HOH A:521 , HOH A:608BINDING SITE FOR RESIDUE HP7 A 550
3AC3SOFTWAREARG A:263 , GLY A:266 , GLN A:273 , HOH A:564BINDING SITE FOR RESIDUE CL A 352
4AC4SOFTWARETHR A:211 , HOH A:362 , HOH A:400 , HOH A:432 , HOH A:512BINDING SITE FOR RESIDUE NA A 353

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q2I)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:104 -Pro A:105
2Tyr A:245 -Pro A:246
3Leu A:347 -Pro A:348

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q2I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q2I)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q2I)

(-) 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:345
 aligned with Q7NQL0_CHRVO | Q7NQL0 from UniProtKB/TrEMBL  Length:352

    Alignment length:352
                                    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  
         Q7NQL0_CHRVO     1 MIVIPPITDRKIRFALVGCGRIANNHFGALEKHADRAELIDVCDIDPAALKAAVERTGARGHASLTDMLAQTDADIVILTTPSGLHPTQSIECSEAGFHVMTEKPMATRWEDGLEMVKAADKAKKHLFVVKQNRRNATLQLLKRAMQEKRFGRIYMVNVNVFWTRPQEYYDAAGWRGTWEFDGGAFMNQASHYVDLLDWLIGPVESVQAYTATLARNIEVEDTGTVSVKWRSGALGSMNVTMLTYPKNLEGSITILGEKGSVRVGGVAVNEIQHWEFSEPHAMDEEIKDASYATTSVYGFGHPLYYDNVIKTMRGEATPETDGREGLKSLELLIAMYLSARDGRRVSLPLDY 352
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------GFO_IDH_MocA-3q2iA01 A:12-131                                                                                           -----------GFO_IDH_MocA_C-3q2iA02 A:143-258                                                                                    ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee....hhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh.eee.hhhhhhhhh...eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee...hhhhhhh.................hhhhhhhhhhhhh.eeeeeeeee..........eeeeeeee....eeeeeee........eeeeeeee..eeeeee.....eeeeeee...hhhhhhhhhhh-------..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q2i A   1 MIVIPPITDRKIRFALVGCGRIANNHFGALEKHADRAELIDVCDIDPAALKAAVERTGARGHASLTDMLAQTDADIVILTTPSGLHPTQSIECSEAGFHVMTEKPMATRWEDGLEMVKAADKAKKHLFVVKQNRRNATLQLLKRAMQEKRFGRIYMVNVNVFWTRPQEYYDAAGWRGTWEFDGGAFMNQASHYVDLLDWLIGPVESVQAYTATLARNIEVEDTGTVSVKWRSGALGSMNVTMLTYPKNLEGSITILGEKGSVRVGGVAVNEIQHWEFSEPHAMDEEIKDAS-------GFGHPLYYDNVIKTMRGEATPETDGREGLKSLELLIAMYLSARDGRRVSLPLDY 351
                                    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|      299       309       319       329       339       349  
                                                                                                                                                                                                                                                                                                                            291     298
   Legend:   → Mismatch (orange background)
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  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 3Q2I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q2I)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: ox_reductase_C (19)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7NQL0_CHRVO | Q7NQL0)
molecular function
    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: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.

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3q2k SIMILAR PROTEIN FROM BORDETELLA PERTUSSIS