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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE AGMATINASE FROM CLOSTRIDIUM DIFFICILE
 
Authors :  K. Palani, S. K. Burley, S. Swaminathan, New York Sgx Research Cent Structural Genomics (Nysgxrc)
Date :  22 Jan 10  (Deposition) - 23 Feb 10  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Agmatinase, Protein Structure Initiative Ii(Psi Ii), Nysgxrc, 11305E, Structural Genomics, New York Sgx Research Center For Structural Genomics, Manganese, Metal-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Palani, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Agmatinase From Clostridium Difficile
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE AGMATINASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidBC - PSGX3 (BC)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 17-292
    GeneCD0891, SPEB
    Organism ScientificCLOSTRIDIUM DIFFICILE
    Organism Taxid272563
    Strain630

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 21)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4PO46Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:111 , ASP A:134 , ASP A:138 , ASP A:215 , MN A:302 , MN A:303BINDING SITE FOR RESIDUE MN A 301
2AC2SOFTWAREASP A:134 , HIS A:136 , ASP A:215 , ASP A:217 , MN A:301 , MN A:303BINDING SITE FOR RESIDUE MN A 302
3AC3SOFTWAREASP A:138 , HIS A:150 , ASP A:215 , GLU A:261 , MN A:301 , MN A:302BINDING SITE FOR RESIDUE MN A 303
4AC4SOFTWAREASN A:236BINDING SITE FOR RESIDUE MN A 304
5AC5SOFTWARETHR A:34 , SER A:35 , ASN A:36 , ARG A:37 , TYR A:143 , HIS A:150 , HOH A:323BINDING SITE FOR RESIDUE PO4 A 305
6AC6SOFTWAREARG A:99 , TYR A:143 , ASN A:144 , ASN A:145 , HOH A:364 , HOH A:419 , HOH A:431BINDING SITE FOR RESIDUE PO4 A 306
7AC7SOFTWAREHOH A:6 , PHE A:26 , GLY A:27 , SER A:44 , ARG A:48 , ASP A:72BINDING SITE FOR RESIDUE MPD A 307

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LHL)

(-) 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:276
 aligned with Q18A84_PEPD6 | Q18A84 from UniProtKB/TrEMBL  Length:292

    Alignment length:276
                                    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      
         Q18A84_PEPD6    17 NYEESNLIVFGVGFDGTTSNRPGARFASSSMRKEFYGLETYSPFLDLDLEDYNICDYGDLEISVGSTEQVLKEIYQETYKIVRDSKVPFMIGGEHLVTLPAFKAVHEKYNDIYVIHFDAHTDLREEYNNSKNSHATVIKRIWDIVGDNKIFQFGIRSGTKEEFKFATEEKHTYMEIGGIDTFENIVNMLNGKNIYLTIDLDVLDASVFPGTGTPEPGGVNYREFQEIFKIIKNSNINIVGCDIVELSPDYDTTGVSTVIACKILRELCLIISDKIK 292
               SCOP domains d3lhla_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee..........hhhhhhhhhhhhhh....ee....ee.hhh.eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh..eeeeee..................hhhhhhhhhhh...eeeeee...hhhhhhhhhh....eeee....hhhhhhhhh...eeeeeee.hhh................hhhhhhhhhhhhhh...eeeeeeee..hhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lhl A  17 NYEESNLIVFGVGFDGTTSNRPGARFASSSmRKEFYGLETYSPFLDLDLEDYNICDYGDLEISVGSTEQVLKEIYQETYKIVRDSKVPFmIGGEHLVTLPAFKAVHEKYNDIYVIHFDAHTDLREEYNNSKNSHATVIKRIWDIVGDNKIFQFGIRSGTKEEFKFATEEKHTYmEIGGIDTFENIVNmLNGKNIYLTIDLDVLDASVFPGTGTPEPGGVNYREFQEIFKIIKNSNINIVGCDIVELSPDYDTTGVSTVIACKILRELCLIISDKIK 292
                                    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                                                    106-MSE                                                                             190-MSE       204-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)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LHL)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q18A84_PEPD6 | Q18A84)
molecular function
    GO:0008783    agmatinase activity    Catalysis of the reaction: agmatine + H(2)O = putrescine + urea.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016813    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amidine, a compound of the form R-C(=NH)-NH2.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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