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(-) Description

Title :  CRYSTAL STRUCTURE OF LIGE-APO FORM 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 :  1.91
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
    Organism Scientific: SPHINGOBIUM SP. SYK-6
    Organism Taxid: 627192
    Synonym: BETA-ARYL ETHER CLEAVING ENZYME

 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, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4YAM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Val A:59 -Pro A:60
2Leu A:143 -Gly A:144
3Gly A:144 -Gly A:145
4Asn B:4 -Asn B:5
5Val B:59 -Pro B:60
6Phe B:142 -Leu B:143
7Gly B:144 -Gly B:145
8Thr B:253 -Gly B:254
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 4YAM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YAM)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........hhhhhhhhhhhhhh..eeeee.....hhhhhh........eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yam A   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
                                                                                                                88-MSE     99-MSE                                                                                                                               233-MSE               


Chain B 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
                 4yam B   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  
                                                                                                               88-MSE     99-MSE                                                                                                                               233-MSE                  


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...hhhhhhhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yam 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  
                                                                                                               88-MSE     99-MSE                                                                                                                               233-MSE                  


Chain D from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........hhhhhhhhhhhhhh..eeeee.....hhhhhh........eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh........................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yam 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 
                                                                                                               88-MSE     99-MSE                                                                                                                               233-MSE
   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 4YAM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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    Asn D:4 - Asn D:5   [ RasMol ]  
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  LIGE_SPHPI | P27457
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 Related Entries

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

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        G2IN93_9SPHN | G2IN93: 4yan

(-) Related Entries Specified in the PDB File

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