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(-) Description

Title :  CRYSTAL STRUCTURE OF DIPICOLINATE SYNTHASE SUBUNIT B FROM BACILLUS HALODURANS C
 
Authors :  B. Nocek, O. Kagan, A. Savchenko, A. Edwards, A. Joachimiak, Midwest C Structural Genomics (Mcsg)
Date :  09 Feb 10  (Deposition) - 23 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Biol. Unit 2:  A  (3x)
Biol. Unit 3:  A  (2x)
Keywords :  Dipicolinate Synthase, Flavoprotein, Psi2, Mcsg, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, O. Kagan, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of Dipicolinate Synthase Subunit B From Bacillus Halodurans C
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPICOLINATE SYNTHASE SUBUNIT B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector: PET15B
    Gene: SPOVFB, BH2402
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665
    Strain: C-125

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A
Biological Unit 2 (3x): A
Biological Unit 3 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 72)
No.NameCountTypeFull Name
1MSE60Mod. Amino AcidSELENOMETHIONINE
2PO412Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 36)
No.NameCountTypeFull Name
1MSE30Mod. Amino AcidSELENOMETHIONINE
2PO46Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 24)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:13 , GLY A:14 , THR A:94 , ASN A:96 , SER A:97 , HOH A:228 , HOH A:248 , HOH A:275BINDING SITE FOR RESIDUE PO4 A 200
2AC2SOFTWAREGLU A:77 , ARG A:119 , ASN A:131BINDING SITE FOR RESIDUE PO4 A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:91 -Pro A:92
2Gln A:188 -Pro A:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LQK)

(-) 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:195
 aligned with Q9KA88_BACHD | Q9KA88 from UniProtKB/TrEMBL  Length:197

    Alignment length:195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     
         Q9KA88_BACHD     1 MNFAGKHVGFGLTGSHCTYHEVLPQMERLVELGAKVTPFVTHTVQTTDTKFGESSEWINKIKQITEEPIVDSMVKAEPFGPKTPLDCMVIAPMTGNSTSKFANAMTDSPVLMGAKATLRNGKPVVVGISTNDALGLNGINIMRLMATKNIYFIPFGQDNPQVKPNSLVARMEALPETIEAALRGQQYQPVLIEKF 195
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Flavoprotein-3lqkA01 A:6-140                                                                                                           ------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhhhh......hhhhhhhhh......eeeeeeehhhhhhhhhh....hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhh...eee..eee.........eee...hhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqk A   1 mNFAGKHVGFGLTGSHCTYHEVLPQmERLVELGAKVTPFVTHTVQTTDTKFGESSEWINKIKQITEEPIVDSmVKAEPFGPKTPLDCmVIAPmTGNSTSKFANAmTDSPVLmGAKATLRNGKPVVVGISTNDALGLNGINImRLmATKNIYFIPFGQDNPQVKPNSLVARmEALPETIEAALRGQQYQPVLIEKF 195
                            |       10        20     |  30        40        50        60        70  |     80       |90  |    100    |  110 |     120       130       140 |  |  150       160       170|      180       190     
                            |                       26-MSE                                         73-MSE         88-MSE|         105-MSE  |                           142-MSE                      171-MSE                    
                            1-MSE                                                                                      93-MSE            112-MSE                          145-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3LQK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9KA88_BACHD | Q9KA88)
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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