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(-) Description

Title :  CRYSTAL STRUCTURE OF A GLUTATHIONE S-TRANSFERASE (ATU5508) FROM AGROBACTERIUM TUMEFACIENS STR. C58 AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  11 Jan 06  (Deposition) - 14 Feb 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  B  (2x)
Keywords :  Thioredoxin Fold, Gst C-Terminal Domain-Like Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kosloff, G. W. Han, S. S. Krishna, R. Schwarzenbacher, M. Fasnacht, M. A. Elsliger, P. Abdubek, S. Agarwalla, E. Ambing, T. Astakhova, H. L. Axelrod, J. M. Canaves, D. Carlton, H. J. Chiu, T. Clayton, M. Didonato, L. Duan, J. Feuerhelm, C. Grittini, S. K. Grzechnik, J. Hale, E. Hampton, J. Haugen, L. Jaroszewski, K. K. Jin, H. Johnson, H. E. Klock, M. W. Knuth, E. Koesema, A. Kreusch, P. Kuhn, I. Levin, D. Mcmullan, M. D. Miller, A. T. Morse, K. Moy, E. Nigoghossian, L. Okach, S. Oommachen, R. Page, J. Paulsen, K. Quijano, R. Reyes, C. L. Rife, E. Sims, G. Spraggon, V. Sridhar, R. C. Stevens, H. Van Den Bedem, J. Velasquez, A. White, G. Wolf, Q. Xu, K. O. Hodgson J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Comparative Structural Analysis Of A Novel Glutathiones-Transferase (Atu5508) From Agrobacterium Tumefaciens At 2. 0 A Resolution.
Proteins V. 65 527 2006
PubMed-ID: 16988933  |  Reference-DOI: 10.1002/PROT.21130

(-) Compounds

Molecule 1 - AGR_PAT_752P
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 15162326
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 176299
    Strain: STR. C58

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1MSE13Mod. Amino AcidSELENOMETHIONINE
2SCN4Ligand/IonTHIOCYANATE ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2SCN4Ligand/IonTHIOCYANATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SCN2Ligand/IonTHIOCYANATE ION
Biological Unit 3 (2, 16)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2SCN4Ligand/IonTHIOCYANATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:177 , TRP A:195 , ARG A:199 , HOH A:358BINDING SITE FOR RESIDUE SCN A 237
2AC2SOFTWAREPHE A:155 , ARG A:200 , HOH A:293 , HOH A:343 , HOH A:462BINDING SITE FOR RESIDUE SCN A 238
3AC3SOFTWAREARG B:200 , THR B:204 , HOH B:314BINDING SITE FOR RESIDUE SCN B 237
4AC4SOFTWAREALA B:177 , TRP B:195 , SER B:198 , ARG B:199 , HOH B:337BINDING SITE FOR RESIDUE SCN B 238

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FNO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:59 -Pro A:60
2Pro B:59 -Pro B:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FNO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FNO)

(-) Exons   (0, 0)

(no "Exon" information available for 2FNO)

(-) 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:239
 aligned with Q7D2W7_AGRFC | Q7D2W7 from UniProtKB/TrEMBL  Length:232

    Alignment length:239
                                   1                                                                                                                                                                                                                                       
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         
         Q7D2W7_AGRFC     - -------MNTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGLMDCGAEKQPVAFMGPPVLIDRERNFAISQMPAIAIYLGERLDILPATVEGRTLSAKIVNDANDVLDELTLNGGREMWTPEKWQEFVPRLQKWIRIFADTGARNGLSAASGFMLGTEKIGVADIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSRRVVATAPLAALNSKSFEEYGNAYCGGEIEKSLRKVAS 232
               SCOP domains ---d2fnoa2 A:1-87 Hypothetical protein AGR_pAT_752p/Atu5508                               d2fnoa1 A:88-236 Hypothetical protein AGR_pAT_752p/Atu5508                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee.......hhhhhhhhhhh...ee..hhhhhhhhhhhhhhhh........eeee....eeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fno A  -2 HHHmEDGmNTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGLmDCGAEKQPVAFmGPPVLIDRERNFAISQmPAIAIYLGERLDILPATVEGRTLSAKIVNDANDVLDELTLNGGREmWTPEKWQEFVPRLQKWIRIFADTGARNGLSAASGFmLGTEKIGVADIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSRRVVATAPLAALNSKSFEEYGNAYCGGEIEKSLRKVAS 236
                               |   | 7        17        27        37       |47        57        67      | 77        87        97       107       117  |    127       137       147       157       167       177       187       197       207       217       227         
                               |   |                                      45-MSE      57-MSE           74-MSE                                       120-MSE                             156-MSE                                                                            
                               1-MSE                                                                                                                                                                                                                                       
                                   5-MSE                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with Q7D2W7_AGRFC | Q7D2W7 from UniProtKB/TrEMBL  Length:232

    Alignment length:234
                              1                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228    
         Q7D2W7_AGRFC     - --MNTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGLMDCGAEKQPVAFMGPPVLIDRERNFAISQMPAIAIYLGERLDILPATVEGRTLSAKIVNDANDVLDELTLNGGREMWTPEKWQEFVPRLQKWIRIFADTGARNGLSAASGFMLGTEKIGVADIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSRRVVATAPLAALNSKSFEEYGNAYCGGEIEKSLRKVAS 232
               SCOP domains d2fnob2 B:3-87 Hypothetical protein AGR_pAT_752p/Atu5508                             d2fnob1 B:88-236 Hypothetical protein AGR_pAT_752p/Atu5508                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.......hhhhhhhhhhh...ee..hhhhhhhhhhhhhhhh........eeee....eeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fno B   3 DGmNTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGLmDCGAEKQPVAFmGPPVLIDRERNFAISQmPAIAIYLGERLDILPATVEGRTLSAKIVNDANDVLDELTLNGGREmWTPEKWQEFVPRLQKWIRIFADTGARNGLSAASGFmLGTEKIGVADIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSRRVVATAPLAALNSKSFEEYGNAYCGGEIEKSLRKVAS 236
                              |     12        22        32        42  |     52    |   62        72 |      82        92       102       112       122       132       142       152   |   162       172       182       192       202       212       222       232    
                              5-MSE                                  45-MSE      57-MSE           74-MSE                                       120-MSE                             156-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FNO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FNO)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7D2W7_AGRFC | Q7D2W7)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

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