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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE POLYSACCHARIDE DEACETYLASE FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  K. Michalska, C. Tesar, J. Bearden, A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg)
Date :  10 May 11  (Deposition) - 22 Jun 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Carbohydrate Esterase Family 4, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Michalska, C. Tesar, J. Bearden, A. Joachimiak
Crystal Structure Of Putative Polysaccharide Deacetylase From Mycobacterium Smegmatis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POLYSACCHARIDE DEACETYLASE
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21 MAGIC
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneMSMEG_4373
    Organism ScientificMYCOBACTERIUM SMEGMATIS
    Organism Taxid246196
    StrainMC2 155

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 40)

Asymmetric/Biological Unit (3, 40)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MSE32Mod. Amino AcidSELENOMETHIONINE
3ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:32 , GLY A:56 , PRO A:240 , PHE A:241BINDING SITE FOR RESIDUE CL A 298
2AC2SOFTWAREASP A:31 , HIS A:104 , HIS A:108 , HOH A:302 , HOH A:303BINDING SITE FOR RESIDUE ZN A 299
3AC3SOFTWAREASP B:31 , ALA B:32 , PRO B:240 , PHE B:241BINDING SITE FOR RESIDUE CL B 298
4AC4SOFTWAREASP B:31 , HIS B:104 , HIS B:108 , HOH B:300 , HOH B:301BINDING SITE FOR RESIDUE ZN B 299
5AC5SOFTWAREALA C:32 , GLY C:56 , PRO C:240 , PHE C:241BINDING SITE FOR RESIDUE CL C 298
6AC6SOFTWAREASP C:31 , HIS C:104 , HIS C:108 , HOH C:300 , HOH C:365BINDING SITE FOR RESIDUE ZN C 299
7AC7SOFTWAREASP D:31 , ALA D:32 , GLY D:56 , PHE D:241BINDING SITE FOR RESIDUE CL D 298
8AC8SOFTWAREASP D:31 , HIS D:104 , HIS D:108 , HOH D:300 , HOH D:301BINDING SITE FOR RESIDUE ZN D 299

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RXZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RXZ)

(-) 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:286
 aligned with A0R0G0_MYCS2 | A0R0G0 from UniProtKB/TrEMBL  Length:297

    Alignment length:286
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287      
         A0R0G0_MYCS2     8 LTPAAPVSWPDGKTCAVAFTFDVDAESPLLTTDPAFADRMGTMSHQAYGPLVGVPRLLGILDEFNVPGTFFVPGYTAHRHPEPIRSIARAGHEIAHHGYLHESLVGADEDTERKILTRGIEALEEVAGVHPVGYRAPMWEMNWHTPKLLAEFGFLYDSTLMDSDHPYELAVGDGSLVELPVSWALDDWQQYCFVPDFSGTGLIETPAKAIELWRAELNAMRDIGGAWVLTNHPFLSGRPGRAAALREFIAEVCAMDDVWVAGMSQIAEHVRAQKLTPRTLTRPELT 293
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhhhhhhh....ee.hhhhh...hhhhhhhhh...ee.........ee........ee...hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rxz A   8 LTPAAPVSWPDGKTCAVAFTFDVDAESPLLTTDPAFADRmGTmSHQAYGPLVGVPRLLGILDEFNVPGTFFVPGYTAHRHPEPIRSIARAGHEIAHHGYLHESLVGADEDTERKILTRGIEALEEVAGVHPVGYRAPmWEmNWHTPKLLAEFGFLYDSTLmDSDHPYELAVGDGSLVELPVSWALDDWQQYCFVPDFSGTGLIETPAKAIELWRAELNAmRDIGGAWVLTNHPFLSGRPGRAAALREFIAEVCAmDDVWVAGmSQIAEHVRAQKLTPRTLTRPELT 293
                                    17        27        37        47  |     57        67        77        87        97       107       117       127       137       147|      157       167|      177       187       197       207       217       227       237       247       257    |  267  |    277       287      
                                                                  47-MSE                                                                                           145-MSE                168-MSE                                                    227-MSE                            262-MSE 270-MSE                   
                                                                     50-MSE                                                                                           148-MSE                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with A0R0G0_MYCS2 | A0R0G0 from UniProtKB/TrEMBL  Length:297

    Alignment length:286
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286      
         A0R0G0_MYCS2     7 ELTPAAPVSWPDGKTCAVAFTFDVDAESPLLTTDPAFADRMGTMSHQAYGPLVGVPRLLGILDEFNVPGTFFVPGYTAHRHPEPIRSIARAGHEIAHHGYLHESLVGADEDTERKILTRGIEALEEVAGVHPVGYRAPMWEMNWHTPKLLAEFGFLYDSTLMDSDHPYELAVGDGSLVELPVSWALDDWQQYCFVPDFSGTGLIETPAKAIELWRAELNAMRDIGGAWVLTNHPFLSGRPGRAAALREFIAEVCAMDDVWVAGMSQIAEHVRAQKLTPRTLTRPEL 292
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhhhhhhh....ee.hhhhh...hhhhhhhhh...ee.........eee......eee...hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rxz B   7 ELTPAAPVSWPDGKTCAVAFTFDVDAESPLLTTDPAFADRmGTmSHQAYGPLVGVPRLLGILDEFNVPGTFFVPGYTAHRHPEPIRSIARAGHEIAHHGYLHESLVGADEDTERKILTRGIEALEEVAGVHPVGYRAPmWEmNWHTPKLLAEFGFLYDSTLmDSDHPYELAVGDGSLVELPVSWALDDWQQYCFVPDFSGTGLIETPAKAIELWRAELNAmRDIGGAWVLTNHPFLSGRPGRAAALREFIAEVCAmDDVWVAGmSQIAEHVRAQKLTPRTLTRPEL 292
                                    16        26        36        46|  |    56        66        76        86        96       106       116       126       136       146 |     156       166 |     176       186       196       206       216       226|      236       246       256     | 266   |   276       286      
                                                                   47-MSE                                                                                           145-MSE                168-MSE                                                    227-MSE                            262-MSE 270-MSE                  
                                                                      50-MSE                                                                                           148-MSE                                                                                                                                            

Chain C from PDB  Type:PROTEIN  Length:287
 aligned with A0R0G0_MYCS2 | A0R0G0 from UniProtKB/TrEMBL  Length:297

    Alignment length:287
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       
         A0R0G0_MYCS2     7 ELTPAAPVSWPDGKTCAVAFTFDVDAESPLLTTDPAFADRMGTMSHQAYGPLVGVPRLLGILDEFNVPGTFFVPGYTAHRHPEPIRSIARAGHEIAHHGYLHESLVGADEDTERKILTRGIEALEEVAGVHPVGYRAPMWEMNWHTPKLLAEFGFLYDSTLMDSDHPYELAVGDGSLVELPVSWALDDWQQYCFVPDFSGTGLIETPAKAIELWRAELNAMRDIGGAWVLTNHPFLSGRPGRAAALREFIAEVCAMDDVWVAGMSQIAEHVRAQKLTPRTLTRPELT 293
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhhhhhhh....ee.hhhhh...hhhhhhhhh...ee.........eeeee..eeeee...hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rxz C   7 ELTPAAPVSWPDGKTCAVAFTFDVDAESPLLTTDPAFADRmGTmSHQAYGPLVGVPRLLGILDEFNVPGTFFVPGYTAHRHPEPIRSIARAGHEIAHHGYLHESLVGADEDTERKILTRGIEALEEVAGVHPVGYRAPmWEmNWHTPKLLAEFGFLYDSTLmDSDHPYELAVGDGSLVELPVSWALDDWQQYCFVPDFSGTGLIETPAKAIELWRAELNAmRDIGGAWVLTNHPFLSGRPGRAAALREFIAEVCAmDDVWVAGmSQIAEHVRAQKLTPRTLTRPELT 293
                                    16        26        36        46|  |    56        66        76        86        96       106       116       126       136       146 |     156       166 |     176       186       196       206       216       226|      236       246       256     | 266   |   276       286       
                                                                   47-MSE                                                                                           145-MSE                168-MSE                                                    227-MSE                            262-MSE 270-MSE                   
                                                                      50-MSE                                                                                           148-MSE                                                                                                                                             

Chain D from PDB  Type:PROTEIN  Length:287
 aligned with A0R0G0_MYCS2 | A0R0G0 from UniProtKB/TrEMBL  Length:297

    Alignment length:287
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       
         A0R0G0_MYCS2     7 ELTPAAPVSWPDGKTCAVAFTFDVDAESPLLTTDPAFADRMGTMSHQAYGPLVGVPRLLGILDEFNVPGTFFVPGYTAHRHPEPIRSIARAGHEIAHHGYLHESLVGADEDTERKILTRGIEALEEVAGVHPVGYRAPMWEMNWHTPKLLAEFGFLYDSTLMDSDHPYELAVGDGSLVELPVSWALDDWQQYCFVPDFSGTGLIETPAKAIELWRAELNAMRDIGGAWVLTNHPFLSGRPGRAAALREFIAEVCAMDDVWVAGMSQIAEHVRAQKLTPRTLTRPELT 293
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------Polysacc_deac_1-3rxzD01 D:18-164                                                                                                                   --------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------Polysacc_deac_1-3rxzD02 D:18-164                                                                                                                   --------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------Polysacc_deac_1-3rxzD03 D:18-164                                                                                                                   --------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------Polysacc_deac_1-3rxzD04 D:18-164                                                                                                                   --------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ...............eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhhhhhhh....ee.hhhhh...hhhhhhhhh...ee.........ee........ee...hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rxz D   7 ELTPAAPVSWPDGKTCAVAFTFDVDAESPLLTTDPAFADRmGTmSHQAYGPLVGVPRLLGILDEFNVPGTFFVPGYTAHRHPEPIRSIARAGHEIAHHGYLHESLVGADEDTERKILTRGIEALEEVAGVHPVGYRAPmWEmNWHTPKLLAEFGFLYDSTLmDSDHPYELAVGDGSLVELPVSWALDDWQQYCFVPDFSGTGLIETPAKAIELWRAELNAmRDIGGAWVLTNHPFLSGRPGRAAALREFIAEVCAmDDVWVAGmSQIAEHVRAQKLTPRTLTRPELT 293
                                    16        26        36        46|  |    56        66        76        86        96       106       116       126       136       146 |     156       166 |     176       186       196       206       216       226|      236       246       256     | 266   |   276       286       
                                                                   47-MSE                                                                                           145-MSE                168-MSE                                                    227-MSE                            262-MSE 270-MSE                   
                                                                      50-MSE                                                                                           148-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 3RXZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: GH_CE (28)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (A0R0G0_MYCS2 | A0R0G0)
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:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.

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