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(-) Description

Title :  CRYSTAL STRUCTURE OF TYPE 1 GLUTAMINE AMIDOTRANSFERASE (GATASE1)-LIKE PROTEIN FROM PLANCTOMYCES LIMNOPHILUS
 
Authors :  K. Michalska, H. Li, J. Bearden, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  12 Apr 11  (Deposition) - 27 Apr 11  (Release) - 27 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Michalska, H. Li, J. Bearden, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Crystal Structure Of Type 1 Glutamine Amidotransferase (Gatase1)-Like Protein From Planctomyces Limnophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - (GATASE1)-LIKE PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: PLIM_2614
    Organism Scientific: PLANCTOMYCES LIMNOPHILUS
    Organism Taxid: 521674
    Strain: DSM 3776

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 45)

Asymmetric Unit (6, 45)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CA4Ligand/IonCALCIUM ION
3CL2Ligand/IonCHLORIDE ION
4GOL8Ligand/IonGLYCEROL
5MSE24Mod. Amino AcidSELENOMETHIONINE
6NA3Ligand/IonSODIUM ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4GOL4Ligand/IonGLYCEROL
5MSE12Mod. Amino AcidSELENOMETHIONINE
6NA-1Ligand/IonSODIUM ION
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4GOL4Ligand/IonGLYCEROL
5MSE12Mod. Amino AcidSELENOMETHIONINE
6NA-1Ligand/IonSODIUM ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:9 , ASP A:55 , ASP A:207 , HOH A:262 , HOH A:263BINDING SITE FOR RESIDUE CA A 257
02AC2SOFTWAREGLU A:176 , HOH A:412 , HOH A:413 , HOH A:415 , HIS B:187BINDING SITE FOR RESIDUE NA A 258
03AC3SOFTWARELEU A:12 , GLU A:13 , THR A:14 , GLY A:17 , GLY A:232BINDING SITE FOR RESIDUE GOL A 259
04AC4SOFTWAREASP A:55 , GLY A:84 , TRP A:85 , ASP A:207 , PRO A:210 , HIS A:211 , TRP A:212 , HOH A:337BINDING SITE FOR RESIDUE GOL A 260
05AC5SOFTWARELYS A:179 , THR A:180 , HIS B:184 , TRP D:169 , HOH D:310BINDING SITE FOR RESIDUE ACT A 261
06AC6SOFTWAREASP B:9 , ASP B:55 , ASP B:207 , HOH B:264 , HOH B:265BINDING SITE FOR RESIDUE CA B 257
07AC7SOFTWAREHOH A:327 , HOH A:416 , SER B:11 , LEU B:12 , TYR B:32 , HOH B:318BINDING SITE FOR RESIDUE CL B 258
08AC8SOFTWARELEU B:12 , GLU B:13 , THR B:14 , GLY B:17 , GLY B:232 , HOH B:299BINDING SITE FOR RESIDUE GOL B 259
09AC9SOFTWAREASP B:55 , GLY B:84 , TRP B:85 , ASP B:207 , PRO B:210 , HIS B:211 , TRP B:212 , HOH B:581BINDING SITE FOR RESIDUE GOL B 260
10BC1SOFTWAREPHE B:173 , LYS B:179 , THR B:180 , HOH B:303 , HOH B:529 , TRP C:169 , HIS C:184BINDING SITE FOR RESIDUE ACT B 261
11BC2SOFTWAREASP C:9 , ASP C:55 , ASP C:207 , HOH C:263 , HOH C:264BINDING SITE FOR RESIDUE CA C 257
12BC3SOFTWAREGLU C:176 , HOH C:429 , HOH C:430 , HOH C:431 , HIS D:187BINDING SITE FOR RESIDUE NA C 258
13BC4SOFTWAREHOH B:273 , HOH B:285 , ASN C:116 , HOH C:337 , HOH C:568BINDING SITE FOR RESIDUE NA C 259
14BC5SOFTWAREASP C:55 , GLY C:84 , TRP C:85 , ASP C:207 , PRO C:210 , HIS C:211 , TRP C:212 , HOH C:489BINDING SITE FOR RESIDUE GOL C 260
15BC6SOFTWARELEU C:12 , GLU C:13 , THR C:14 , GLY C:17 , GLY C:232 , HOH C:305 , HOH C:490BINDING SITE FOR RESIDUE GOL C 261
16BC7SOFTWARELYS C:179 , THR C:180 , HOH C:270 , HIS D:184BINDING SITE FOR RESIDUE ACT C 262
17BC8SOFTWAREASP D:9 , ASP D:55 , ASP D:207 , HOH D:262 , HOH D:263BINDING SITE FOR RESIDUE CA D 257
18BC9SOFTWARELEU D:12 , TYR D:32 , HOH D:296 , HOH D:330BINDING SITE FOR RESIDUE CL D 258
19CC1SOFTWAREASP D:55 , GLY D:84 , TRP D:85 , ASP D:207 , PRO D:210 , HIS D:211 , TRP D:212 , HOH D:272BINDING SITE FOR RESIDUE GOL D 259
20CC2SOFTWARELEU D:12 , GLU D:13 , THR D:14 , GLY D:17 , GLY D:232 , HOH D:451BINDING SITE FOR RESIDUE GOL D 260
21CC3SOFTWARETRP A:169 , GLY D:178 , LYS D:179 , THR D:180BINDING SITE FOR RESIDUE ACT D 261

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RHT)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:210 -His A:211
2Pro B:210 -His B:211
3Pro C:210 -His C:211
4Pro D:210 -His D:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RHT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RHT)

(-) Exons   (0, 0)

(no "Exon" information available for 3RHT)

(-) 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
 aligned with D5SQH6_PLAL2 | D5SQH6 from UniProtKB/TrEMBL  Length:256

    Alignment length: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  
         D5SQH6_PLAL2     3 RVLYCGDTSLETAAGYLAGLMTSWQWEFDYIPSHVGLDVGELLAKQDLVILSDYPAERMTAQAIDQLVTMVKAGCGLVMLGGWESYHGLGGNWDQTLLAEVLPVDIKSADDRINFDQPTLAIPAAINSVSHPILQNLPWEDRPPTIGGLNRIAAKAKAQTLLMARVWRPTFSLEHGKTTWEHADHHPLLVVGEAGTGRVAAFASDVAPHWVGGLVDWGDERVTSQAPGAGAIEVGNLYSQFFRQMLEWVAKS 254
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhh....eee........hhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhh..ee......eee....eeeee.hhhhhhh................eee..ee....eeeeeeeee..eee....eee..eeeeeeeeeeeee..eeeeee........hhhhhhh...eeee.......eeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rht A   3 RVLYCGDTSLETAAGYLAGLmTSWQWEFDYIPSHVGLDVGELLAKQDLVILSDYPAERmTAQAIDQLVTmVKAGCGLVmLGGWESYHGLGGNWDQTLLAEVLPVDIKSADDRINFDQPTLAIPAAINSVSHPILQNLPWEDRPPTIGGLNRIAAKAKAQTLLmARVWRPTFSLEHGKTTWEHADHHPLLVVGEAGTGRVAAFASDVAPHWVGGLVDWGDERVTSQAPGAGAIEVGNLYSQFFRQmLEWVAKS 254
                                    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  
                                               23-MSE                                61-MSE     72-MSE   81-MSE                                                                             165-MSE                                                                           247-MSE   


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with D5SQH6_PLAL2 | D5SQH6 from UniProtKB/TrEMBL  Length:256

    Alignment length: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  
         D5SQH6_PLAL2     3 RVLYCGDTSLETAAGYLAGLMTSWQWEFDYIPSHVGLDVGELLAKQDLVILSDYPAERMTAQAIDQLVTMVKAGCGLVMLGGWESYHGLGGNWDQTLLAEVLPVDIKSADDRINFDQPTLAIPAAINSVSHPILQNLPWEDRPPTIGGLNRIAAKAKAQTLLMARVWRPTFSLEHGKTTWEHADHHPLLVVGEAGTGRVAAFASDVAPHWVGGLVDWGDERVTSQAPGAGAIEVGNLYSQFFRQMLEWVAKS 254
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhh...eeee........hhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhh..ee......eee....eeeee.hhhhhhh................eee..ee....eeeeeeeee..eee....eee..eeeeeeeeeeeee..eeeeee........hhhhhhh...eeee.......eeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rht B   3 RVLYCGDTSLETAAGYLAGLmTSWQWEFDYIPSHVGLDVGELLAKQDLVILSDYPAERmTAQAIDQLVTmVKAGCGLVmLGGWESYHGLGGNWDQTLLAEVLPVDIKSADDRINFDQPTLAIPAAINSVSHPILQNLPWEDRPPTIGGLNRIAAKAKAQTLLmARVWRPTFSLEHGKTTWEHADHHPLLVVGEAGTGRVAAFASDVAPHWVGGLVDWGDERVTSQAPGAGAIEVGNLYSQFFRQmLEWVAKS 254
                                    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  
                                               23-MSE                                61-MSE     72-MSE   81-MSE                                                                             165-MSE                                                                           247-MSE   


Chain C from PDB  Type:PROTEIN  Length:252
 aligned with D5SQH6_PLAL2 | D5SQH6 from UniProtKB/TrEMBL  Length:256

    Alignment length: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  
         D5SQH6_PLAL2     3 RVLYCGDTSLETAAGYLAGLMTSWQWEFDYIPSHVGLDVGELLAKQDLVILSDYPAERMTAQAIDQLVTMVKAGCGLVMLGGWESYHGLGGNWDQTLLAEVLPVDIKSADDRINFDQPTLAIPAAINSVSHPILQNLPWEDRPPTIGGLNRIAAKAKAQTLLMARVWRPTFSLEHGKTTWEHADHHPLLVVGEAGTGRVAAFASDVAPHWVGGLVDWGDERVTSQAPGAGAIEVGNLYSQFFRQMLEWVAKS 254
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhh...eeee........hhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhh..ee......eee....eeeee.hhhhhhh................eee..ee....eeeeeeeee..eee....eee..eeeeeeeeeeeee..eeeeee........hhhhhhh...eeee.......eeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rht C   3 RVLYCGDTSLETAAGYLAGLmTSWQWEFDYIPSHVGLDVGELLAKQDLVILSDYPAERmTAQAIDQLVTmVKAGCGLVmLGGWESYHGLGGNWDQTLLAEVLPVDIKSADDRINFDQPTLAIPAAINSVSHPILQNLPWEDRPPTIGGLNRIAAKAKAQTLLmARVWRPTFSLEHGKTTWEHADHHPLLVVGEAGTGRVAAFASDVAPHWVGGLVDWGDERVTSQAPGAGAIEVGNLYSQFFRQmLEWVAKS 254
                                    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  
                                               23-MSE                                61-MSE     72-MSE   81-MSE                                                                             165-MSE                                                                           247-MSE   


Chain D from PDB  Type:PROTEIN  Length:252
 aligned with D5SQH6_PLAL2 | D5SQH6 from UniProtKB/TrEMBL  Length:256

    Alignment length: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  
         D5SQH6_PLAL2     3 RVLYCGDTSLETAAGYLAGLMTSWQWEFDYIPSHVGLDVGELLAKQDLVILSDYPAERMTAQAIDQLVTMVKAGCGLVMLGGWESYHGLGGNWDQTLLAEVLPVDIKSADDRINFDQPTLAIPAAINSVSHPILQNLPWEDRPPTIGGLNRIAAKAKAQTLLMARVWRPTFSLEHGKTTWEHADHHPLLVVGEAGTGRVAAFASDVAPHWVGGLVDWGDERVTSQAPGAGAIEVGNLYSQFFRQMLEWVAKS 254
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) DUF1355-3rhtD01 D:3-154                                                                                                                                 ---------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) DUF1355-3rhtD02 D:3-154                                                                                                                                 ---------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) DUF1355-3rhtD03 D:3-154                                                                                                                                 ---------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) DUF1355-3rhtD04 D:3-154                                                                                                                                 ---------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeee.......hhhhhhhhhhh...eeee........hhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhh..ee......eee....eeeee.hhhhhhh................eee..ee....eeeeeeeee..eee....eee..eeeeeeeeeeeee..eeeeee........hhhhhhh...eeee.......eeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rht D   3 RVLYCGDTSLETAAGYLAGLmTSWQWEFDYIPSHVGLDVGELLAKQDLVILSDYPAERmTAQAIDQLVTmVKAGCGLVmLGGWESYHGLGGNWDQTLLAEVLPVDIKSADDRINFDQPTLAIPAAINSVSHPILQNLPWEDRPPTIGGLNRIAAKAKAQTLLmARVWRPTFSLEHGKTTWEHADHHPLLVVGEAGTGRVAAFASDVAPHWVGGLVDWGDERVTSQAPGAGAIEVGNLYSQFFRQmLEWVAKS 254
                                    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  
                                               23-MSE                                61-MSE     72-MSE   81-MSE                                                                             165-MSE                                                                           247-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 3RHT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RHT)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Glutaminase_I (73)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (D5SQH6_PLAL2 | D5SQH6)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  3rht
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