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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIPICOLINATE SYNTHASE CHAIN B FROM BACILLUS CEREUS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BCR215.
 
Authors :  S. Vorobiev, S. Lew, M. Abashidze, J. Seetharaman, H. Wang, C. Ciccosanti, E. L. Foote, L. Mao, R. Xiao, T. B. Acton, G. T Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  29 Mar 10  (Deposition) - 14 Apr 10  (Release) - 14 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Nesg, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Vorobiev, S. Lew, M. Abashidze, J. Seetharaman, H. Wang, C. Ciccosanti, E. L. Foote, R. Xiao, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Dipicolinate Synthase Chain B From Bacillus Cereus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPICOLINATE SYNTHASE, B CHAIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 21-23C
    Expression System Strain: BL21 (DE3) +MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BC_3800
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 226900
    Strain: ATCC 14579/DSM 31

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 67)

Asymmetric/Biological Unit (2, 67)
No.NameCountTypeFull Name
1MSE60Mod. Amino AcidSELENOMETHIONINE
2PO47Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:119 , HOH A:415 , ASN F:131 , LYS F:163BINDING SITE FOR RESIDUE PO4 A 305
2AC2SOFTWARETHR C:13 , GLY C:14 , SER C:41 , TYR C:42 , THR C:94 , ASN C:96 , SER C:97BINDING SITE FOR RESIDUE PO4 C 301
3AC3SOFTWAREASN A:131 , ARG C:119 , HOH C:787BINDING SITE FOR RESIDUE PO4 C 306
4AC4SOFTWARETHR D:13 , GLY D:14 , SER D:41 , TYR D:42 , THR D:94 , ASN D:96 , SER D:97BINDING SITE FOR RESIDUE PO4 D 302
5AC5SOFTWARETHR E:13 , GLY E:14 , SER E:41 , THR E:94 , ASN E:96 , SER E:97BINDING SITE FOR RESIDUE PO4 E 303
6AC6SOFTWAREASN B:131 , ARG E:119 , HOH E:788BINDING SITE FOR RESIDUE PO4 E 307
7AC7SOFTWARETHR F:13 , GLY F:14 , SER F:41 , TYR F:42 , THR F:94 , ASN F:96 , SER F:97BINDING SITE FOR RESIDUE PO4 F 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Ala A:91 -Pro A:92
2Gln A:188 -Pro A:189
3Ala B:91 -Pro B:92
4Gln B:188 -Pro B:189
5Ala C:91 -Pro C:92
6Gln C:188 -Pro C:189
7Ala D:91 -Pro D:92
8Gln D:188 -Pro D:189
9Ala E:91 -Pro E:92
10Gln E:188 -Pro E:189
11Ala F:91 -Pro F:92
12Gln F:188 -Pro F:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MCU)

(-) Sequences/Alignments

Asymmetric/Biological 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:185
 aligned with Q819Z6_BACCR | Q819Z6 from UniProtKB/TrEMBL  Length:199

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
         Q819Z6_BACCR     2 SLKGKRIGFGFTGSHCTYEEVMPHLEKLIAEGAEVRPVVSYTVQSTNTRFGEGAEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCMVIAPLTGNSMSKFANAMTDSPVLMAAKATLRNGKPVVLAVSTNDALGLNGVNLMRLMATKNIYFVPFGQDAPEKKPNSMVARMELLEDTVLEALQGKQLQPVVVEKFRYM 198
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..hhhhhh.hhhhhhhhhhh..eeeeee..------------hhhhhhhhhhh......hhhhhhhhh......eeeeeeehhhhhhhhhh....hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhh..eee..eee.........eee...hhhhhhhhhhh.........hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcu A   2 SLKGKRIGFGFTGSHCTYEEVmPHLEKLIAEGAEVRPVVSY------------AEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCmVIAPLTGNSmSKFANAmTDSPVLmAAKATLRNGKPVVLAVSTNDALGLNGVNLmRLmATKNIYFVPFGQDAPEKKPNSmVARmELLEDTVLEALQGKQLQPVVVEKFRYm 198
                                    11        21 |      31        41|        -   |    61        71        81      | 91      |101   |   111|      121       131       141|  |   151       161     | 171       181       191      |
                                                23-MSE             42           55                               88-MSE    98-MSE  |      |                           142-MSE                  167-MSE                        198-MSE
                                                                                                                                 105-MSE  |                              145-MSE                   171-MSE                       
                                                                                                                                        112-MSE                                                                                  


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with Q819Z6_BACCR | Q819Z6 from UniProtKB/TrEMBL  Length:199

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
         Q819Z6_BACCR     2 SLKGKRIGFGFTGSHCTYEEVMPHLEKLIAEGAEVRPVVSYTVQSTNTRFGEGAEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCMVIAPLTGNSMSKFANAMTDSPVLMAAKATLRNGKPVVLAVSTNDALGLNGVNLMRLMATKNIYFVPFGQDAPEKKPNSMVARMELLEDTVLEALQGKQLQPVVVEKFRYM 198
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..hhhhhh.hhhhhhhhhhh..eeeeee...----------.hhhhhhhhhhh......hhhhhhhhh......eeeeeeehhhhhhhhhh....hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhh..eee..ee..........eee...hhhhhhhhhh..........hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcu B   2 SLKGKRIGFGFTGSHCTYEEVmPHLEKLIAEGAEVRPVVSYT----------GAEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCmVIAPLTGNSmSKFANAmTDSPVLmAAKATLRNGKPVVLAVSTNDALGLNGVNLmRLmATKNIYFVPFGQDAPEKKPNSmVARmELLEDTVLEALQGKQLQPVVVEKFRYm 198
                                    11        21 |      31        41 |       -  |     61        71        81      | 91      |101   |   111|      121       131       141|  |   151       161     | 171       181       191      |
                                                23-MSE              43         54                                88-MSE    98-MSE  |      |                           142-MSE                  167-MSE                        198-MSE
                                                                                                                                 105-MSE  |                              145-MSE                   171-MSE                       
                                                                                                                                        112-MSE                                                                                  


Chain C from PDB  Type:PROTEIN  Length:186
 aligned with Q819Z6_BACCR | Q819Z6 from UniProtKB/TrEMBL  Length:199

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
         Q819Z6_BACCR     2 SLKGKRIGFGFTGSHCTYEEVMPHLEKLIAEGAEVRPVVSYTVQSTNTRFGEGAEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCMVIAPLTGNSMSKFANAMTDSPVLMAAKATLRNGKPVVLAVSTNDALGLNGVNLMRLMATKNIYFVPFGQDAPEKKPNSMVARMELLEDTVLEALQGKQLQPVVVEKFRYM 198
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..hhhhh..hhhhhhhhhhh..eeeeee...-----------hhhhhhhhhhh......hhhhhhhhh......eeeeeeeehhhhhhhhh....hhhhhhhhhhhh....eeeeeee......hhhhhhhhhh...eee..ee..........eee...hhhhhhhhhh..........hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcu C   2 SLKGKRIGFGFTGSHCTYEEVmPHLEKLIAEGAEVRPVVSYT-----------AEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCmVIAPLTGNSmSKFANAmTDSPVLmAAKATLRNGKPVVLAVSTNDALGLNGVNLmRLmATKNIYFVPFGQDAPEKKPNSmVARmELLEDTVLEALQGKQLQPVVVEKFRYm 198
                                    11        21 |      31        41 |       -   |    61        71        81      | 91      |101   |   111|      121       131       141|  |   151       161     | 171       181       191      |
                                                23-MSE              43          55                               88-MSE    98-MSE  |      |                           142-MSE                  167-MSE                        198-MSE
                                                                                                                                 105-MSE  |                              145-MSE                   171-MSE                       
                                                                                                                                        112-MSE                                                                                  


Chain D from PDB  Type:PROTEIN  Length:188
 aligned with Q819Z6_BACCR | Q819Z6 from UniProtKB/TrEMBL  Length:199

    Alignment length:199
                                                                                                                                                                                                                               199   
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       | 
         Q819Z6_BACCR     2 SLKGKRIGFGFTGSHCTYEEVMPHLEKLIAEGAEVRPVVSYTVQSTNTRFGEGAEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCMVIAPLTGNSMSKFANAMTDSPVLMAAKATLRNGKPVVLAVSTNDALGLNGVNLMRLMATKNIYFVPFGQDAPEKKPNSMVARMELLEDTVLEALQGKQLQPVVVEKFRYMN-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...hhhhh.hhhhhhhhhhh..eeeeee...-----------.hhhhhhhhhhh.....hhhhhhhhh......eeeeeeeehhhhhhhhh....hhhhhhhhhhhh....eeeeeee......hhhhhhhhhh...eee..ee..........eee...hhhhhhhhhh..........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcu D   2 SLKGKRIGFGFTGSHCTYEEVmPHLEKLIAEGAEVRPVVSYT-----------AEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCmVIAPLTGNSmSKFANAmTDSPVLmAAKATLRNGKPVVLAVSTNDALGLNGVNLmRLmATKNIYFVPFGQDAPEKKPNSmVARmELLEDTVLEALQGKQLQPVVVEKFRYmNL 200
                                    11        21 |      31        41 |       -   |    61        71        81      | 91      |101   |   111|      121       131       141|  |   151       161     | 171       181       191      |  
                                                23-MSE              43          55                               88-MSE    98-MSE  |      |                           142-MSE                  167-MSE                        198-MSE
                                                                                                                                 105-MSE  |                              145-MSE                   171-MSE                         
                                                                                                                                        112-MSE                                                                                    


Chain E from PDB  Type:PROTEIN  Length:183
 aligned with Q819Z6_BACCR | Q819Z6 from UniProtKB/TrEMBL  Length:199

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
         Q819Z6_BACCR     2 SLKGKRIGFGFTGSHCTYEEVMPHLEKLIAEGAEVRPVVSYTVQSTNTRFGEGAEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCMVIAPLTGNSMSKFANAMTDSPVLMAAKATLRNGKPVVLAVSTNDALGLNGVNLMRLMATKNIYFVPFGQDAPEKKPNSMVARMELLEDTVLEALQGKQLQPVVVEKFRYM 198
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...hhhhhhhhhhhhhhhhh..eeeeee..--------------hhhhhhhhhh.....hhhhhhhhh......eeeeeeehhhhhhhhhh....hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhh..eee..ee..........eee...hhhhhhhhhhh.........hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcu E   2 SLKGKRIGFGFTGSHCTYEEVmPHLEKLIAEGAEVRPVVSY--------------WIKKIEEITGFKAINSIVGAEPLGPKIPLDCmVIAPLTGNSmSKFANAmTDSPVLmAAKATLRNGKPVVLAVSTNDALGLNGVNLmRLmATKNIYFVPFGQDAPEKKPNSmVARmELLEDTVLEALQGKQLQPVVVEKFRYm 198
                                    11        21 |      31        41|        -     |  61        71        81      | 91      |101   |   111|      121       131       141|  |   151       161     | 171       181       191      |
                                                23-MSE             42             57                             88-MSE    98-MSE  |      |                           142-MSE                  167-MSE                        198-MSE
                                                                                                                                 105-MSE  |                              145-MSE                   171-MSE                       
                                                                                                                                        112-MSE                                                                                  


Chain F from PDB  Type:PROTEIN  Length:187
 aligned with Q819Z6_BACCR | Q819Z6 from UniProtKB/TrEMBL  Length:199

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
         Q819Z6_BACCR     2 SLKGKRIGFGFTGSHCTYEEVMPHLEKLIAEGAEVRPVVSYTVQSTNTRFGEGAEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCMVIAPLTGNSMSKFANAMTDSPVLMAAKATLRNGKPVVLAVSTNDALGLNGVNLMRLMATKNIYFVPFGQDAPEKKPNSMVARMELLEDTVLEALQGKQLQPVVVEKFRYMN 199
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----Flavoprotein-3mcuF01 F:6-139                                                                                                          ------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----Flavoprotein-3mcuF02 F:6-139                                                                                                          ------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) ----Flavoprotein-3mcuF03 F:6-139                                                                                                          ------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) ----Flavoprotein-3mcuF04 F:6-139                                                                                                          ------------------------------------------------------------ Pfam domains (4)
           Pfam domains (5) ----Flavoprotein-3mcuF05 F:6-139                                                                                                          ------------------------------------------------------------ Pfam domains (5)
           Pfam domains (6) ----Flavoprotein-3mcuF06 F:6-139                                                                                                          ------------------------------------------------------------ Pfam domains (6)
         Sec.struct. author .....eeeeee...hhhhh.hhhhhhhhhhh..eeeeee...-----------.hhhhhhhhhh......hhhhhhhhh......eeeeeeeehhhhhhhhh....hhhhhhhhhhhh....eeeeeee......hhhhhhhhhh...eee..ee..........eee...hhhhhhhhhhh.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mcu F   2 SLKGKRIGFGFTGSHCTYEEVmPHLEKLIAEGAEVRPVVSYT-----------AEWIKKIEEITGFKAINSIVGAEPLGPKIPLDCmVIAPLTGNSmSKFANAmTDSPVLmAAKATLRNGKPVVLAVSTNDALGLNGVNLmRLmATKNIYFVPFGQDAPEKKPNSmVARmELLEDTVLEALQGKQLQPVVVEKFRYmN 199
                                    11        21 |      31        41 |       -   |    61        71        81      | 91      |101   |   111|      121       131       141|  |   151       161     | 171       181       191      | 
                                                23-MSE              43          55                               88-MSE    98-MSE  |      |                           142-MSE                  167-MSE                        198-MSE
                                                                                                                                 105-MSE  |                              145-MSE                   171-MSE                        
                                                                                                                                        112-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 3MCU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Flavoprotein] (5)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q819Z6_BACCR | Q819Z6)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.

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