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(-) Description

Title :  CRYSTAL STRUCTURE OF LIGL 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 :  1.50
Chains :  Asym./Biol. Unit :  A,B
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, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LIGL, SLG_33660
    Organism Scientific: SPHINGOBIUM SP. SYK-6
    Organism Taxid: 627192
    Synonym: CALPHA-DEHYDROGENASE

 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
1NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:12 , SER A:15 , GLY A:16 , ILE A:17 , ASP A:36 , ILE A:37 , ARG A:38 , HIS A:41 , LEU A:63 , ASP A:64 , VAL A:65 , ASN A:91 , ALA A:92 , GLY A:93 , ILE A:114 , THR A:142 , ALA A:143 , SER A:144 , TYR A:158 , LYS A:162 , PRO A:188 , GLY A:189 , PRO A:190 , ILE A:191 , SER A:193 , ARG A:194 , ILE A:195 , ASN A:201 , HOH A:709 , HOH A:710 , HOH A:714 , HOH A:716 , HOH A:833 , HOH A:852binding site for residue NAD A 500
2AC2SOFTWAREGLY B:12 , SER B:15 , GLY B:16 , ILE B:17 , ASP B:36 , ILE B:37 , ARG B:38 , HIS B:41 , LEU B:63 , ASP B:64 , VAL B:65 , ASN B:91 , ALA B:92 , GLY B:93 , ILE B:114 , THR B:142 , ALA B:143 , SER B:144 , TYR B:158 , LYS B:162 , PRO B:188 , GLY B:189 , PRO B:190 , ILE B:191 , SER B:193 , ARG B:194 , ILE B:195 , HOH B:687 , HOH B:697 , HOH B:715 , HOH B:789 , HOH B:832 , HOH B:837binding site for residue NAD B 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:84 -Pro A:85
2Gly B:84 -Pro B:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YAG)

(-) 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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yag A   1 MDIAGTTAFITGGASGIGFGIAQRLLANGARLVLADIRQDHLDEARQFFEERQQGRNVHTIRLDVSDRAQMAEAARECEAVMGGPDILINNAGIDPSGPFKDATYQDWDYGLAINLMGPINGIMAFTPGMRARGRGGHIVNTASLAGLTPMPSFMAIYATAKAAVITLTETIRDSMAEDNIGVTVLMPGPIKSRIHESGQNRPERFRAGSGLAETEQQLAKRVVADNWMEPTEVGDMIVDAIVHNKLYVSTHGNWRETCEARFQALLDSMP 271
                                    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 


Chain B from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yag B   1 MDIAGTTAFITGGASGIGFGIAQRLLANGARLVLADIRQDHLDEARQFFEERQQGRNVHTIRLDVSDRAQMAEAARECEAVMGGPDILINNAGIDPSGPFKDATYQDWDYGLAINLMGPINGIMAFTPGMRARGRGGHIVNTASLAGLTPMPSFMAIYATAKAAVITLTETIRDSMAEDNIGVTVLMPGPIKSRIHESGQNRPERFRAGSGLAETEQQLAKRVVADNWMEPTEVGDMIVDAIVHNKLYVSTHGNWRETCEARFQALLDSMP 271
                                    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
   Legend:   → Mismatch (orange background)
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  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 4YAG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        C0SUJ9_9SPHN | C0SUJ9: 4yae 4yai

(-) Related Entries Specified in the PDB File

4y98 4y9d 4ya6 4yac 4yae 4yai 4yam 4yan 4yap 4yav