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(-) Description

Title :  STRUCTURE OF LMO2462, A LISTERIA MONOCYTOGENES AMIDOHYDROLASE FAMILY PUTATIVE DIPEPTIDASE
 
Authors :  S. M. Anderson, Z. Wawrzak, O. Onopriyenko, J. Hasseman, A. Edwards, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  16 Feb 10  (Deposition) - 09 Mar 10  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Dipeptidase, Metallo-Dependent Hydrolase, Lysteria, Csgid, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Anderson, Z. Wawrzak, O. Onopriyenko, J. Hasseman, A. Edwards, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid
Structure Of Lmo2462, A Listeria Monocytogenes Amidohydrolase Family Putative Dipeptidase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LMO2462 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Gene: LMO2462
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
    Strain: EGD-E

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:105 , HIS A:172 , HIS A:192 , ASP A:261 , ZN A:310 , HOH A:393 , HOH A:395BINDING SITE FOR RESIDUE ZN A 309
2AC2SOFTWAREHIS A:7 , ASP A:9 , GLU A:105 , ZN A:309BINDING SITE FOR RESIDUE ZN A 310
3AC3SOFTWAREGLU B:105 , HIS B:172 , HIS B:192 , ZN B:310 , HOH B:420 , HOH B:431BINDING SITE FOR RESIDUE ZN B 309
4AC4SOFTWAREHIS B:7 , ASP B:9 , GLU B:105 , ZN B:309 , HOH B:431BINDING SITE FOR RESIDUE ZN B 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LU2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LU2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LU2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LU2)

(-) Exons   (0, 0)

(no "Exon" information available for 3LU2)

(-) 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:309
 aligned with Q8Y4H9_LISMO | Q8Y4H9 from UniProtKB/TrEMBL  Length:308

    Alignment length:309
                             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       299         
         Q8Y4H9_LISMO     - -MRVIDTHCDALYKLQAGKGKYTFQDAEELDVNFERLIEAKMLLQGFAIFLDEDIPVEHKWKKAVEQVNIFKQHVLHKGGIIHHVKKWCDLENLPEDKIGAMLTLEGIEPIGRDLDKLTQLLDGGVLSVGLTWNNANLAADGIMEERGAGLTRFGKDIIHLLNERKVFTDVSHLSVKAFWETLEQAEFVIASHSSAKAICAHPRNLDDEQIKAMIEHDAMIHVIFHPLFTTNDGVADIEDVIRHIDHICELGGMKNIGFGSDFDGIPDHVKGLEHAGKYQNFLETLGKHYTKEEVEGFASRNFLNHLPK 308
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhh.............hhhhhhhhheeeeeeee.........hhhhhhhhhhhhhhhhh.hhhh.eee..hhhhhhh.....eeeeeeee.hhhhh.hhhhhhhhhhh.eeeee.....................hhhhhhhhhhhhhh..eee....hhhhhhhhhhhh..eee...............hhhhhhhhhhh..eeee..hhhhh......hhhhhhhhhhhhhhh.hhh.eee...............hhhhhhhhhhhhh...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lu2 A   0 AmRVIDTHCDALYKLQAGKGKYTFQDAEELDVNFERLIEAKmLLQGFAIFLDEDIPVEHKWKKAVEQVNIFKQHVLHKGGIIHHVKKWCDLENLPEDKIGAmLTLEGIEPIGRDLDKLTQLLDGGVLSVGLTWNNANLAADGImEERGAGLTRFGKDIIHLLNERKVFTDVSHLSVKAFWETLEQAEFVIASHSSAKAICAHPRNLDDEQIKAmIEHDAmIHVIFHPLFTTNDGVADIEDVIRHIDHICELGGmKNIGFGSDFDGIPDHVKGLEHAGKYQNFLETLGKHYTKEEVEGFASRNFLNHLPK 308
                             |       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       299         
                             |                                      41-MSE                                                     101-MSE                                   143-MSE                                                               213-MSE |                               253-MSE                                                   
                             1-MSE                                                                                                                                                                                                                   219-MSE                                                                                     


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with Q8Y4H9_LISMO | Q8Y4H9 from UniProtKB/TrEMBL  Length:308

    Alignment length:309
                             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       299         
         Q8Y4H9_LISMO     - -MRVIDTHCDALYKLQAGKGKYTFQDAEELDVNFERLIEAKMLLQGFAIFLDEDIPVEHKWKKAVEQVNIFKQHVLHKGGIIHHVKKWCDLENLPEDKIGAMLTLEGIEPIGRDLDKLTQLLDGGVLSVGLTWNNANLAADGIMEERGAGLTRFGKDIIHLLNERKVFTDVSHLSVKAFWETLEQAEFVIASHSSAKAICAHPRNLDDEQIKAMIEHDAMIHVIFHPLFTTNDGVADIEDVIRHIDHICELGGMKNIGFGSDFDGIPDHVKGLEHAGKYQNFLETLGKHYTKEEVEGFASRNFLNHLPK 308
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Peptidase_M19-3lu2B01 B:1-308                                                                                                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) -Peptidase_M19-3lu2B02 B:1-308                                                                                                                                                                                                                                                                                        Pfam domains (2)
         Sec.struct. author ...eeeeeehhhhhhhhh..............hhhhhhhhheeeeeeee......hhhhhhhhhhhhhhhhhhhh.hhhh.eee..hhhhhhh.....eeeeeeee.hhhhh.hhhhhhhhhhh.eeeee.....................hhhhhhhhhhhhhh..eee....hhhhhhhhhhhh..eee...............hhhhhhhhhhh..eeee..hhhhhh.....hhhhhhhhhhhhhhh.hhh.eee...............hhhhhhhhhhhhh...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lu2 B   0 AmRVIDTHCDALYKLQAGKGKYTFQDAEELDVNFERLIEAKmLLQGFAIFLDEDIPVEHKWKKAVEQVNIFKQHVLHKGGIIHHVKKWCDLENLPEDKIGAmLTLEGIEPIGRDLDKLTQLLDGGVLSVGLTWNNANLAADGImEERGAGLTRFGKDIIHLLNERKVFTDVSHLSVKAFWETLEQAEFVIASHSSAKAICAHPRNLDDEQIKAmIEHDAmIHVIFHPLFTTNDGVADIEDVIRHIDHICELGGmKNIGFGSDFDGIPDHVKGLEHAGKYQNFLETLGKHYTKEEVEGFASRNFLNHLPK 308
                             |       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       299         
                             1-MSE                                  41-MSE                                                     101-MSE                                   143-MSE                                                               213-MSE |                               253-MSE                                                   
                                                                                                                                                                                                                                                     219-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 3LU2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LU2)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8Y4H9_LISMO | Q8Y4H9)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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