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(-) Description

Title :  CRYSTAL STRUCTURE OF LIGD IN COMPLEX WITH NADH FROM SPHINGOBIUM SP. STRAIN SYK-6
 
Authors :  J. H. Pereira, R. P. Mcandrew, R. A. Heins, K. L. Sale, B. A. Simmons, P. D.
Date :  17 Feb 15  (Deposition) - 09 Mar 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Short Chain Dehydrogenase/Reductase Sdr Family, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Pereira, R. A. Heins, D. L. Gall, R. P. Mcandrew, K. Deng, K. C. Holland, T. J. Donohue, D. R. Noguera, B. A. Simmons, K. L. Sale, J. Ralph, P. D. Adams
Structural And Biochemical Characterization Of The Early An Late Enzymes In The Lignin Beta-Aryl Ether Cleavage Pathway From Sphingobium Sp. Syk-6.
J. Biol. Chem. V. 291 10228 2016
PubMed-ID: 26940872  |  Reference-DOI: 10.1074/JBC.M115.700427

(-) Compounds

Molecule 1 - C ALPHA-DEHYDROGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LIGD
    Organism Scientific: SPHINGOBIUM SP. SYK-6
    Organism Taxid: 627192

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , SER A:16 , GLY A:17 , ALA A:18 , ASP A:37 , ARG A:39 , LEU A:62 , ASP A:63 , ILE A:64 , ALA A:92 , VAL A:94 , HOH A:509binding site for residue NAD A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y9D)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:271 -Met A:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y9D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y9D)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y9D)

(-) 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:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y9d A   3 DFQDQVAFITGGASGAGFGQAKVFGQAGAKIVVADVRAEAVEKAVAELEGLGITAHGIVLDIMDREAYARAADEVEAVFGQAPTLLSNTAGVNSFGPIEKTTYDDFDWIIGVNLNGVINGMVTFVPRMIASGRPGHIVTVSSLGGFMGSALAGPYSAAKAASINLMEGYRQGLEKYGIGVSVCTPANIHGLEPEKLAEAIKKGVEDNALYIIPYPEVREGLEKHFQAIIDSVAPM 272
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       227       237       247       257       267     
                                                                                                                                                                                                                     190|                                              
                                                                                                                                                                                                                      226
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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 4Y9D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y9D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y9D)

(-) Gene Ontology  (2, 2)

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 Related Entries

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UniProtKB/TrEMBL
        G2IN91_9SPHN | G2IN91: 4y98

(-) Related Entries Specified in the PDB File

4y98