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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE CARBOXYNORSPERMIDINE DECARBOXYLASE PROTEIN FROM SINORHIZOBIUM MELILOTI
 
Authors :  C. Chang, X. Xu, H. Cui, S. Chin, A. Savchenko, A. Edwards, A. Joachimiak Center For Structural Genomics (Mcsg)
Date :  29 Apr 10  (Deposition) - 30 Jun 10  (Release) - 30 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Psi2, Mcsg, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Carboxynorspermidine Decarboxylase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, X. Xu, H. Cui, S. Chin, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of Putative Carboxynorspermidine Decarboxylase Protein From Sinorhizobium Meliloti
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE CARBOXYNORSPERMIDINE DECARBOXYLASE PROTEIN
    Chains: A, B
    EC Number: 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PET DERIVATIVE
    Gene: NSPC, RB1551, SM_B21631, SMB21631
    Organism Common: SINORHIZOBIUM MELILOTI
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 382

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric/Biological Unit (2, 23)
No.NameCountTypeFull Name
1MSE21Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:198 , GLY A:199 , GLY A:232 , GLU A:233 , TYR A:324 , HOH A:372BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREGLY B:199 , GLY B:232 , GLU B:233 , TYR B:324 , HOH B:374 , HOH B:392BINDING SITE FOR RESIDUE SO4 B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MT1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:4 -Pro A:5
2Leu A:280 -Pro A:281
3Thr B:4 -Pro B:5
4Leu B:280 -Pro B:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MT1)

(-) Exons   (0, 0)

(no "Exon" information available for 3MT1)

(-) 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:346
 aligned with Q92TG9_RHIME | Q92TG9 from UniProtKB/TrEMBL  Length:365

    Alignment length:364
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
         Q92TG9_RHIME     2 IETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQVSSSSFDLADPARPFSRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNGKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 365
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhh....eeee.hhhhhhhhhhhh..eeeeee......hhhhhhhhh.eeee.hhhhhhhhhhhhh..eeeeee...----------------.....hhhhhhhhhhhh.eeee...--..hhhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhh.eeee..hhhhhh..eeeeeeeeeeee...eeeee..hhhhhhhhhhhh............eeeeee........eeeeeee........eeee............hhhhh...eeeee.....eeeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mt1 A   2 IETPYYLIDKAKLTRNmERIAHVREKSGAKALLALKCFATWSVFDLmRDYmDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQ----------------RLGEWDVPKVERVmDRINGFmIHNN--NKDFGLFDRmLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNGKNLAIVDSSIEAHmLDLLIYRETAKVLPNEGSHSYmICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTmVKKNWFNGVKmPAIAIRELDGSVRTVREFTYADYEQSLS 365
                                    11      | 21        31        41      | 51|       61        71        81        91       101       111       121 |       -       141       151 |     161  |  | 171    |  181       191       201       211       221       231       241       251       261     | 271       281       291       301       311       321    |  331     | 341       351       361    
                                           18-MSE                        48-MSE                                                                    123              140          153-MSE  | 164  |      176-MSE                                                                                    267-MSE               289-MSE                              326-MSE    337-MSE                        
                                                                             52-MSE                                                                                                     160-MSE167                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:348
 aligned with Q92TG9_RHIME | Q92TG9 from UniProtKB/TrEMBL  Length:365

    Alignment length:365
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360     
         Q92TG9_RHIME     1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQVSSSSFDLADPARPFSRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNGKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 365
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------                ----------------------------------------------------------------------Orn_DAP_Arg_deC-3mt1B01 B:210-342                                                                                                    ----------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------                ----------------------------------------------------------------------Orn_DAP_Arg_deC-3mt1B02 B:210-342                                                                                                    ----------------------- Pfam domains (2)
         Sec.struct. author .....eeeeehhhhhhhhhhhhhhhhhhh.ee.ee.....hhhhhhhhhh...eeee.hhhhhhhhhhhh..eeeee....hhhhhhhhhhhh.eeee.hhhhhhhhh......eeeee....----------------.....hhhhhhh......eee........hhhhhhhhhhhhhhhhhhhhhhh.eee............hhhhhhhhhhhhhhhhh.eeee..hhhhhh..eeeeeeeeeee..-.eeeee..hhhhhhhhhhhhh...........eeeeee........eeeeeee........eeee......hhhhh.hhhhh...eeeee.....eeeee..hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mt1 B   1 mIETPYYLIDKAKLTRNmERIAHVREKSGAKALLALKCFATWSVFDLmRDYmDGTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQ----------------RLGEWDVPKVERVmDRINGFmIHNNCENKDFGLFDRmLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYN-KNLAIVDSSIEAHmLDLLIYRETAKVLPNEGSHSYmICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTmVKKNWFNGVKmPAIAIRELDGSVRTVREFTYADYEQSLS 365
                            |       10       |20        30        40       |50 |      60        70        80        90       100       110       120  |      -       140       150  |    160       170     | 180       190       200       210       220       230       240       250 | |   260      |270       280       290       300       310       320     | 330      |340       350       360     
                            1-MSE           18-MSE                        48-MSE                                                                    123              140          153-MSE  |             176-MSE                                                                     252 |          267-MSE               289-MSE                              326-MSE    337-MSE                        
                                                                              52-MSE                                                                                                     160-MSE                                                                                       254
   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 3MT1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MT1)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Orn_DAP_Arg_deC] (18)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q92TG9_RHIME | Q92TG9)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0006596    polyamine biosynthetic process    The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.
    GO:0008295    spermidine biosynthetic process    The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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