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(-) Description

Title :  CRYSTAL STRUCTURE OF LIGE IN COMPLEX WITH GLUTATHIONE (GSH) 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) - 16 Dec 15  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Glutathione-S-Transferase B-Etherase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Helmich, J. H. Pereira, D. L. Gall, R. A. Heins, R. P. Mcandrew, C. Bingman, K. Deng, K. C. Holland, D. R. Noguera, B. A. Simmons, K. L. Sale, J. Ralph, T. J. Donohue, P. D. Adams, G. N. Phillips
Structural Basis Of Stereospecificity In The Bacterial Enzymatic Cleavage Of Beta-Aryl Ether Bonds In Lignin.
J. Biol. Chem. V. 291 5234 2016
PubMed-ID: 26637355  |  Reference-DOI: 10.1074/JBC.M115.694307

(-) Compounds

Molecule 1 - BETA-ETHERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LIGE, SLG_08660
    Organism Scientific: SPHINGOBIUM SP. SYK-6
    Organism Taxid: 627192

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GSH4Ligand/IonGLUTATHIONE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GSH2Ligand/IonGLUTATHIONE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GSH2Ligand/IonGLUTATHIONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:12 , TYR A:23 , PHE A:45 , ILE A:48 , VAL A:59 , PRO A:60 , ASP A:71 , SER A:72 , TYR A:133 , ARG A:138 , HOH A:412binding site for residue GSH A 300
2AC2SOFTWARELEU B:12 , SER B:21 , TYR B:23 , PHE B:45 , ILE B:48 , ARG B:58 , VAL B:59 , PRO B:60 , ASP B:71 , SER B:72 , ARG B:138binding site for residue GSH B 300
3AC3SOFTWARELEU C:12 , TYR C:23 , PHE C:45 , ILE C:48 , ARG C:58 , VAL C:59 , PRO C:60 , ASP C:71 , SER C:72 , TYR C:133 , ARG C:138 , HOH C:422binding site for residue GSH C 300
4AC4SOFTWARELEU D:12 , TYR D:23 , ILE D:48 , ARG D:58 , VAL D:59 , PRO D:60 , ASP D:71 , SER D:72 , TYR D:133 , ARG D:138 , HOH D:434binding site for residue GSH D 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Asn A:4 -Asn A:5
2Val A:59 -Pro A:60
3Phe A:142 -Leu A:143
4Gly A:144 -Gly A:145
5Thr A:253 -Gly A:254
6Val B:59 -Pro B:60
7Leu B:143 -Gly B:144
8Gly B:144 -Gly B:145
9Asn C:4 -Asn C:5
10Val C:59 -Pro C:60
11Thr C:253 -Gly C:254
12Asn D:4 -Asn D:5
13Val D:59 -Pro D:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YAN)

(-) 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:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..........hhhhhhhhhhhhhh..eeeee.....hhhhhh........eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yan A   4 NNTITLYDLQLESGCTISPYVWRTKYALKHKGFDIDIVPGGFTGILERTGGRSERVPVIVDDGEWVLDSWVIAEYLDEKYPDRPMLFEGPTQKNLMKFLDNWLWSTAVGPWFRCYILDYHDLSLPQDRDYVRWSREQWFLGGQRLEDVQAGREDRLPLVPPTLEPFRRILAETKWLGGDQPNFADYSALAVFLWTASVARTPPLTEDDPLRDWLDRGFDLFDGLGRHPGMNPLFGLKLREGDPEPFVRQTGP 255
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253  


Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........hhhhhhhhhhhhhh..eeeee.....hhhhhh........eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yan B   3 RNNTITLYDLQLESGCTISPYVWRTKYALKHKGFDIDIVPGGFTGILERTGGRSERVPVIVDDGEWVLDSWVIAEYLDEKYPDRPMLFEGPTQKNLMKFLDNWLWSTAVGPWFRCYILDYHDLSLPQDRDYVRWSREQWFLGGQRLEDVQAGREDRLPLVPPTLEPFRRILAETKWLGGDQPNFADYSALAVFLWTASVARTPPLTEDDPLRDWLDRGFDLFDGLGRHPGMNPLFGLKLREGDPEPFVRQ 252
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252


Chain C from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..........hhhhhhhhhhhhhh..eeeee.....hhhhhh........eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yan C   4 NNTITLYDLQLESGCTISPYVWRTKYALKHKGFDIDIVPGGFTGILERTGGRSERVPVIVDDGEWVLDSWVIAEYLDEKYPDRPMLFEGPTQKNLMKFLDNWLWSTAVGPWFRCYILDYHDLSLPQDRDYVRWSREQWFLGGQRLEDVQAGREDRLPLVPPTLEPFRRILAETKWLGGDQPNFADYSALAVFLWTASVARTPPLTEDDPLRDWLDRGFDLFDGLGRHPGMNPLFGLKLREGDPEPFVRQTGP 255
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253  


Chain D from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........hhhhhhhhhhhhhhh.eeeee.....hhhhhh........eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh........................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yan D   4 NNTITLYDLQLESGCTISPYVWRTKYALKHKGFDIDIVPGGFTGILERTGGRSERVPVIVDDGEWVLDSWVIAEYLDEKYPDRPMLFEGPTQKNLMKFLDNWLWSTAVGPWFRCYILDYHDLSLPQDRDYVRWSREQWFLGGQRLEDVQAGREDRLPLVPPTLEPFRRILAETKWLGGDQPNFADYSALAVFLWTASVARTPPLTEDDPLRDWLDRGFDLFDGLGRHPGMNPLFGLKLREGDPEPFVRQTG 254
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4YAN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4YAN)

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 Related Entries

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        G2IN93_9SPHN | G2IN93: 4yam

(-) Related Entries Specified in the PDB File

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