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(-) Description

Title :  CRYSTAL STRUCTURE OF DIPICOLINATE SYNTHASE SUBUNIT A (NP_243269.1) FROM BACILLUS HALODURANS AT 2.10 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  14 May 08  (Deposition) - 08 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Np_243269. 1, Dipicolinate Synthase Subunit A, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Alanine Dehydrogenase/Pnt, C-Terminal Domain Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Dipicolinate Synthase Subunit A (Np_243269. 1) From Bacillus Halodurans At 2. 10 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPICOLINATE SYNTHASE SUBUNIT A
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Vector Type: PLASMID
    Gene: NP_243269.1, SPOVFA, BH2403
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 58)

Asymmetric Unit (3, 58)
No.NameCountTypeFull Name
1EDO13Ligand/Ion1,2-ETHANEDIOL
2MSE44Mod. Amino AcidSELENOMETHIONINE
3TAR1Ligand/IonD(-)-TARTARIC ACID
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2MSE22Mod. Amino AcidSELENOMETHIONINE
3TAR1Ligand/IonD(-)-TARTARIC ACID
Biological Unit 2 (2, 30)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2MSE22Mod. Amino AcidSELENOMETHIONINE
3TAR-1Ligand/IonD(-)-TARTARIC ACID
Biological Unit 3 (3, 58)
No.NameCountTypeFull Name
1EDO13Ligand/Ion1,2-ETHANEDIOL
2MSE44Mod. Amino AcidSELENOMETHIONINE
3TAR1Ligand/IonD(-)-TARTARIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY B:163 , HOH B:348 , HOH B:417BINDING SITE FOR RESIDUE EDO B 293
02AC2SOFTWAREGLN A:16 , LEU A:62 , LEU A:63 , PRO A:64 , ILE A:65 , TYR A:100 , LEU A:122BINDING SITE FOR RESIDUE EDO A 293
03AC3SOFTWAREARG B:278 , PHE D:150 , ASP D:214 , HIS D:236 , HOH D:302 , HOH D:365BINDING SITE FOR RESIDUE EDO D 293
04AC4SOFTWAREARG C:171 , ALA C:174 , ALA C:175 , ARG D:171BINDING SITE FOR RESIDUE EDO C 293
05AC5SOFTWAREGLN D:16 , LEU D:62 , LEU D:63 , PRO D:64 , ILE D:65 , TYR D:100 , LEU D:122 , HOH D:300BINDING SITE FOR RESIDUE EDO D 294
06AC6SOFTWAREGLN B:16 , LEU B:62 , LEU B:63 , PRO B:64 , ILE B:65 , TYR B:100 , HOH B:312BINDING SITE FOR RESIDUE EDO B 294
07AC7SOFTWAREARG A:125 , HOH A:328 , HOH A:416 , SER B:187BINDING SITE FOR RESIDUE EDO A 294
08AC8SOFTWAREGLN C:16 , LEU C:62 , LEU C:63 , PRO C:64 , ILE C:65 , TYR C:100 , LEU C:122 , HOH C:322BINDING SITE FOR RESIDUE EDO C 294
09AC9SOFTWAREARG D:15 , ASN D:132 , THR D:136 , GLY D:266 , PRO D:268 , HOH D:452 , HOH D:453 , HOH D:459BINDING SITE FOR RESIDUE EDO D 295
10BC1SOFTWARETYR B:253 , ARG B:257BINDING SITE FOR RESIDUE EDO B 295
11BC2SOFTWAREASP B:214 , HOH B:311 , HOH B:385 , HOH B:391BINDING SITE FOR RESIDUE EDO B 296
12BC3SOFTWAREARG A:278 , PHE C:150 , ASP C:214 , HOH C:302BINDING SITE FOR RESIDUE EDO C 295
13BC4SOFTWAREGLY A:163 , ARG A:164 , HOH A:304 , HOH A:310 , HOH A:354 , HOH A:477BINDING SITE FOR RESIDUE TAR A 295

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D4O)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:245 -Pro A:246
2Lys B:245 -Pro B:246
3Lys C:245 -Pro C:246
4Lys D:245 -Pro D:246

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D4O)

(-) Exons   (0, 0)

(no "Exon" information available for 3D4O)

(-) 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:290
 aligned with Q9KA87_BACHD | Q9KA87 from UniProtKB/TrEMBL  Length:292

    Alignment length:292
                             1                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  
         Q9KA87_BACHD     - -MLTGKHVVIIGGDARQLEIIRKLSTFDAKISLVGFDQLDDGFIGVTKMRIDEVDWNTVDAILLPISGTNEAGKVDTIFSNESIVLTEEMIEKTPNHCVVYSGISNTYLNQCMKKTNRTLVKLMERDDIAIYNSIPTAEGTIMMAIQHTDFTIHGANVAVLGLGRVGMSVARKFAALGAKVKVGARESDLLARIAEMGMEPFHISKAAQELRDVDVCINTIPALVVTANVLAEMPSHTFVIDLASKPGGTDFRYAEKRGIKALLVPGLPGIVAPKTAGRILADVLVKLLAEP 291
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d4oA01 A:0-125,A:273-291 NAD(P)-binding   Rossmann-like Domain                                                               3d4oA02 A:126-272 NAD(P)-binding Rossmann-like Domain                                                                                              3d4oA01             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..hhhhhhhhhhhhhh..eeeee......--....eeehhhhhhhhhh.eee.......................hhhhhhh.....eeee...hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh..eeee..hhhhhh....eeee.......hhhhhhhh....eeee........hhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4o A   0 GmLTGKHVVIIGGDARQLEIIRKLSTFDAKISLVGFDQLD--FIGVTKmRIDEVDWNTVDAILLPISGTNEAGKVDTIFSNESIVLTEEmIEKTPNHCVVYSGISNTYLNQCmKKTNRTLVKLmERDDIAIYNSIPTAEGTImmAIQHTDFTIHGANVAVLGLGRVGmSVARKFAALGAKVKVGARESDLLARIAEmGmEPFHISKAAQELRDVDVCINTIPALVVTANVLAEmPSHTFVIDLASKPGGTDFRYAEKRGIKALLVPGLPGIVAPKTAGRILADVLVKLLAEP 291
                             |       9        19        29        39  |     49        59        69        79        89        99       109  |    119   |   129       139  ||   149       159       169       179       189      |199       209       219       229   |   239       249       259       269       279       289  
                             |                                    39 42     |                                       89-MSE                112-MSE    123-MSE            142-MSE                  167-MSE                      196-MSE                              233-MSE                                                      
                             1-MSE                                         48-MSE                                                                                        143-MSE                                                198-MSE                                                                                         


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with Q9KA87_BACHD | Q9KA87 from UniProtKB/TrEMBL  Length:292

    Alignment length:292
                             1                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  
         Q9KA87_BACHD     - -MLTGKHVVIIGGDARQLEIIRKLSTFDAKISLVGFDQLDDGFIGVTKMRIDEVDWNTVDAILLPISGTNEAGKVDTIFSNESIVLTEEMIEKTPNHCVVYSGISNTYLNQCMKKTNRTLVKLMERDDIAIYNSIPTAEGTIMMAIQHTDFTIHGANVAVLGLGRVGMSVARKFAALGAKVKVGARESDLLARIAEMGMEPFHISKAAQELRDVDVCINTIPALVVTANVLAEMPSHTFVIDLASKPGGTDFRYAEKRGIKALLVPGLPGIVAPKTAGRILADVLVKLLAEP 291
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d4oB01 B:0-125,B:273-291 NAD(P)-binding  Rossmann-like Domain                                                                3d4oB02 B:126-272 NAD(P)-binding Rossmann-like Domain                                                                                              3d4oB01             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..hhhhhhhhhhhhhh..eeeee......-....eeeehhhhhhhhhh.eee.......................hhhhhhh.....eeee...hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh..eeee..hhhhhh....eeee.......hhhhhhhh....eeee........hhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4o B   0 GmLTGKHVVIIGGDARQLEIIRKLSTFDAKISLVGFDQLD-GFIGVTKmRIDEVDWNTVDAILLPISGTNEAGKVDTIFSNESIVLTEEmIEKTPNHCVVYSGISNTYLNQCmKKTNRTLVKLmERDDIAIYNSIPTAEGTImmAIQHTDFTIHGANVAVLGLGRVGmSVARKFAALGAKVKVGARESDLLARIAEmGmEPFHISKAAQELRDVDVCINTIPALVVTANVLAEmPSHTFVIDLASKPGGTDFRYAEKRGIKALLVPGLPGIVAPKTAGRILADVLVKLLAEP 291
                             |       9        19        29        39 |      49        59        69        79        89        99       109  |    119   |   129       139  ||   149       159       169       179       189      |199       209       219       229   |   239       249       259       269       279       289  
                             1-MSE                                39 |     48-MSE                                   89-MSE                112-MSE    123-MSE            142-MSE                  167-MSE                      196-MSE                              233-MSE                                                      
                                                                    41                                                                                                   143-MSE                                                198-MSE                                                                                         


Chain C from PDB  Type:PROTEIN  Length:291
 aligned with Q9KA87_BACHD | Q9KA87 from UniProtKB/TrEMBL  Length:292

    Alignment length:291
                             1                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289 
         Q9KA87_BACHD     - -MLTGKHVVIIGGDARQLEIIRKLSTFDAKISLVGFDQLDDGFIGVTKMRIDEVDWNTVDAILLPISGTNEAGKVDTIFSNESIVLTEEMIEKTPNHCVVYSGISNTYLNQCMKKTNRTLVKLMERDDIAIYNSIPTAEGTIMMAIQHTDFTIHGANVAVLGLGRVGMSVARKFAALGAKVKVGARESDLLARIAEMGMEPFHISKAAQELRDVDVCINTIPALVVTANVLAEMPSHTFVIDLASKPGGTDFRYAEKRGIKALLVPGLPGIVAPKTAGRILADVLVKLLAE 290
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d4oC01 C:0-125,C:273-290 NAD(P)-binding Rossmann-like Domain                                                                 3d4oC02 C:126-272 NAD(P)-binding Rossmann-like Domain                                                                                              3d4oC01            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..hhhhhhhhhhhhhh..eeeee...........eeeehhhhhhhhhh.eee.......................hhhhhhh.....eeee...hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh..eeee..hhhhhh....eeee.......hhhhhhhh....eeee........hhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4o C   0 GmLTGKHVVIIGGDARQLEIIRKLSTFDAKISLVGFDQLDDGFIGVTKmRIDEVDWNTVDAILLPISGTNEAGKVDTIFSNESIVLTEEmIEKTPNHCVVYSGISNTYLNQCmKKTNRTLVKLmERDDIAIYNSIPTAEGTImmAIQHTDFTIHGANVAVLGLGRVGmSVARKFAALGAKVKVGARESDLLARIAEmGmEPFHISKAAQELRDVDVCINTIPALVVTANVLAEmPSHTFVIDLASKPGGTDFRYAEKRGIKALLVPGLPGIVAPKTAGRILADVLVKLLAE 290
                             |       9        19        29        39        49        59        69        79        89        99       109  |    119   |   129       139  ||   149       159       169       179       189      |199       209       219       229   |   239       249       259       269       279       289 
                             1-MSE                                         48-MSE                                   89-MSE                112-MSE    123-MSE            142-MSE                  167-MSE                      196-MSE                              233-MSE                                                     
                                                                                                                                                                         143-MSE                                                198-MSE                                                                                        


Chain D from PDB  Type:PROTEIN  Length:290
 aligned with Q9KA87_BACHD | Q9KA87 from UniProtKB/TrEMBL  Length:292

    Alignment length:291
                             1                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289 
         Q9KA87_BACHD     - -MLTGKHVVIIGGDARQLEIIRKLSTFDAKISLVGFDQLDDGFIGVTKMRIDEVDWNTVDAILLPISGTNEAGKVDTIFSNESIVLTEEMIEKTPNHCVVYSGISNTYLNQCMKKTNRTLVKLMERDDIAIYNSIPTAEGTIMMAIQHTDFTIHGANVAVLGLGRVGMSVARKFAALGAKVKVGARESDLLARIAEMGMEPFHISKAAQELRDVDVCINTIPALVVTANVLAEMPSHTFVIDLASKPGGTDFRYAEKRGIKALLVPGLPGIVAPKTAGRILADVLVKLLAE 290
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d4oD01 D:0-125,D:273-290 NAD(P)-binding  Rossmann-like Domain                                                                3d4oD02 D:126-272 NAD(P)-binding Rossmann-like Domain                                                                                              3d4oD01            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....hhhhhhhhhhhh..eeeee......-....eee.hhhhhhhhhh.eee..........ee........ee.hhhhhh......eeee...hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh..eeee..hhhhhhhhh.eeee.......hhhhhhhh....eeee........hhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4o D   0 GmLTGKHVVIIGGDARQLEIIRKLSTFDAKISLVGFDQLD-GFIGVTKmRIDEVDWNTVDAILLPISGTNEAGKVDTIFSNESIVLTEEmIEKTPNHCVVYSGISNTYLNQCmKKTNRTLVKLmERDDIAIYNSIPTAEGTImmAIQHTDFTIHGANVAVLGLGRVGmSVARKFAALGAKVKVGARESDLLARIAEmGmEPFHISKAAQELRDVDVCINTIPALVVTANVLAEmPSHTFVIDLASKPGGTDFRYAEKRGIKALLVPGLPGIVAPKTAGRILADVLVKLLAE 290
                             |       9        19        29        39 |      49        59        69        79        89        99       109  |    119   |   129       139  ||   149       159       169       179       189      |199       209       219       229   |   239       249       259       269       279       289 
                             1-MSE                                39 |     48-MSE                                   89-MSE                112-MSE    123-MSE            142-MSE                  167-MSE                      196-MSE                              233-MSE                                                     
                                                                    41                                                                                                   143-MSE                                                198-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  (0, 0)

(no "SCOP Domain" information available for 3D4O)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: Rossmann fold (7312)
(-)
Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)
(-)
Bacillus halodurans. Organism_taxid: 86665. (1)
1a3d4oA02A:126-272
1b3d4oB02B:126-272
1c3d4oC02C:126-272
1d3d4oD02D:126-272
1e3d4oB01B:0-125,B:273-291
1f3d4oC01C:0-125,C:273-290
1g3d4oA01A:0-125,A:273-291
1h3d4oD01D:0-125,D:273-290

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D4O)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3D4O)

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