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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE DIPEPTIDASE AC, METALLO PEPTIDASE. MEROPS FAMILY M19
 
Authors :  R. Zhang, C. Hatzos, L. Freeman, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  25 Nov 08  (Deposition) - 23 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dipeptidase Ac, Metallo Peptidase. Merops Family M19, Structural Genomics, Mcsg, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, C. Hatzos, L. Freeman, A. Joachimiak
The Crystal Structure Of The Dipeptidase Ac, Metallo Peptidase. Merops Family M19
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPEPTIDASE AC. METALLO PEPTIDASE. MEROPS FAMILY M19
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 272943
    Strain: 2.4.1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:137 , HIS A:210 , HIS A:231 , MG A:357 , HOH A:416 , HOH A:492 , HOH A:582BINDING SITE FOR RESIDUE MG A 356
2AC2SOFTWAREHIS A:11 , ASP A:13 , GLU A:137 , MG A:356 , HOH A:463 , HOH A:582BINDING SITE FOR RESIDUE MG A 357
3AC3SOFTWAREHIS B:11 , ASP B:13 , GLU B:137 , MG B:357 , HOH B:464BINDING SITE FOR RESIDUE MG B 356
4AC4SOFTWAREGLU B:137 , HIS B:210 , HIS B:231 , MG B:356 , HOH B:383 , HOH B:422BINDING SITE FOR RESIDUE MG B 357

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:178 -Pro A:179
2Pro B:75 -Pro B:76
3Phe B:178 -Pro B:179

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FDG)

(-) 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:338
 aligned with Q3IZQ3_RHOS4 | Q3IZQ3 from UniProtKB/TrEMBL  Length:355

    Alignment length:353
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   
         Q3IZQ3_RHOS4     3 ETIPVFDGHNDFLLRLLRNPANRETIWLKGDGTGHLDLPRMKEGGFAGGFFAIYVPSPQAHDAAHFEAMMDAPPFELPLPPMIRAEQAQPVALAMAGHLLWMERAARGRFKVCRTAAEVRSCHADGIVSGIMHMEGAEAIGADLDALHLFHSLGLRSLGPVWSRPTVFGHGVPFRFPGSPDTGEGLTEAGRRLVAECNRLKIMLDLSHLNEKGFDDVARLSDAPLVATHSNAHAVTPSTRNLTDRQLAMIRESRGMVGLNFATSFLREDGRRSAEMGWEPVLRHLDHLIDRLGEDHVGMGSDFDGATIPQGIADVTGLPALQAAMRAHGYDEPLMRKLCHENWYGLLERSWGA 355
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fdgA00 A:3-355 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhhhh..hhhhhhhh.......hhhhhhhhheeeeeeee.....---------------.ee.......hhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhh.eeeeeeee........hhhhhhhhhhheeeee...............ee..........hhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhh....ee...............hhhhhhhhhhh..eeee..hhhhhh..........hhhhhhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdg A   3 ETIPVFDGHNDFLLRLLRNPANRETIWLKGDGTGHLDLPRMKEGGFAGGFFAIYVPSP---------------PFELPLPPMIRAEQAQPVALAMAGHLLWMERAARGRFKVCRTAAEVRSCHADGIVSGIMHMEGAEAIGADLDALHLFHSLGLRSLGPVWSRPTVFGHGVPFRFPGSPDTGEGLTEAGRRLVAECNRLKIMLDLSHLNEKGFDDVARLSDAPLVATHSNAHAVTPSTRNLTDRQLAMIRESRGMVGLNFATSFLREDGRRSAEMGWEPVLRHLDHLIDRLGEDHVGMGSDFDGATIPQGIADVTGLPALQAAMRAHGYDEPLMRKLCHENWYGLLERSWGA 355
                                    12        22        32        42        52       | -         -   |    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   
                                                                                    60              76                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:348
 aligned with Q3IZQ3_RHOS4 | Q3IZQ3 from UniProtKB/TrEMBL  Length:355

    Alignment length:353
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   
         Q3IZQ3_RHOS4     3 ETIPVFDGHNDFLLRLLRNPANRETIWLKGDGTGHLDLPRMKEGGFAGGFFAIYVPSPQAHDAAHFEAMMDAPPFELPLPPMIRAEQAQPVALAMAGHLLWMERAARGRFKVCRTAAEVRSCHADGIVSGIMHMEGAEAIGADLDALHLFHSLGLRSLGPVWSRPTVFGHGVPFRFPGSPDTGEGLTEAGRRLVAECNRLKIMLDLSHLNEKGFDDVARLSDAPLVATHSNAHAVTPSTRNLTDRQLAMIRESRGMVGLNFATSFLREDGRRSAEMGWEPVLRHLDHLIDRLGEDHVGMGSDFDGATIPQGIADVTGLPALQAAMRAHGYDEPLMRKLCHENWYGLLERSWGA 355
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fdgB00 B:3-355 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhhhh..hhhhhhhh.......hhhhhhhhheeeeeeeee....-----hhhhhhh....ee.......hhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhh.eeeeeeee........hhhhhhhhhhheeeee...............ee..........hhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhh....ee...............hhhhhhhhhhh..eeee..hhhhhh..........hhhhhhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdg B   3 ETIPVFDGHNDFLLRLLRNPANRETIWLKGDGTGHLDLPRMKEGGFAGGFFAIYVPSP-----AHFEAMMDAPPFELPLPPMIRAEQAQPVALAMAGHLLWMERAARGRFKVCRTAAEVRSCHADGIVSGIMHMEGAEAIGADLDALHLFHSLGLRSLGPVWSRPTVFGHGVPFRFPGSPDTGEGLTEAGRRLVAECNRLKIMLDLSHLNEKGFDDVARLSDAPLVATHSNAHAVTPSTRNLTDRQLAMIRESRGMVGLNFATSFLREDGRRSAEMGWEPVLRHLDHLIDRLGEDHVGMGSDFDGATIPQGIADVTGLPALQAAMRAHGYDEPLMRKLCHENWYGLLERSWGA 355
                                    12        22        32        42        52       | -   |    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   
                                                                                    60    66
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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 3FDG)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q3IZQ3_RHOS4 | Q3IZQ3)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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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