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(-) Description

Title :  CRYSTAL STRUCTURE OF METALLO PEPTIDASE FROM RHODOBACTER SPHAEROIDES LIGANDED WITH PHOSPHINATE MIMIC OF DIPEPTIDE L-ALA-D-ALA
 
Authors :  A. A. Fedorov, E. V. Fedorov, J. Cummings, F. M. Raushel, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  25 Feb 10  (Deposition) - 09 Mar 10  (Release) - 09 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Nysgrc, Target 9523C, Metallo Peptidase, Phosphinate Inhibitor, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, J. Cummings, F. M. Raushel, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Metallo Peptidase From Rhodobacter Sphaeroides Liganded With Phosphinate Mimic Of Dipeptide L-Ala-D-Ala
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 Taxid: 562
    Gene: RHOS4_24130, RSP_0802
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 272943
    Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1LY02Ligand/Ion(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC ACID
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1LY01Ligand/Ion(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1LY01Ligand/Ion(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:11 , ASP A:13 , TYR A:56 , HIS A:63 , GLU A:137 , TRP A:164 , PHE A:176 , HIS A:210 , HIS A:231 , ARG A:242 , PHE A:267 , ASP A:304 , GLY A:307 , ZN A:364 , ZN A:365BINDING SITE FOR RESIDUE LY0 A 363
2AC2SOFTWAREHIS A:11 , ASP A:13 , GLU A:137 , LY0 A:363 , ZN A:365BINDING SITE FOR RESIDUE ZN A 364
3AC3SOFTWAREGLU A:137 , HIS A:210 , HIS A:231 , LY0 A:363 , ZN A:364BINDING SITE FOR RESIDUE ZN A 365
4AC4SOFTWAREHIS B:11 , ASP B:13 , TYR B:56 , HIS B:63 , GLU B:137 , TRP B:164 , PHE B:176 , HIS B:210 , HIS B:231 , ARG B:242 , PHE B:267 , ASP B:304 , GLY B:307 , ZN B:364 , ZN B:365BINDING SITE FOR RESIDUE LY0 B 363
5AC5SOFTWAREHIS B:11 , ASP B:13 , GLU B:137 , LY0 B:363 , ZN B:365BINDING SITE FOR RESIDUE ZN B 364
6AC6SOFTWAREGLU B:137 , HIS B:210 , HIS B:231 , LY0 B:363 , ZN B:364BINDING SITE FOR RESIDUE ZN B 365

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LY0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:75 -Pro A:76
2Phe A:178 -Pro A:179
3Pro B:75 -Pro B:76
4Phe B:178 -Pro B:179

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LY0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LY0)

(-) Exons   (0, 0)

(no "Exon" information available for 3LY0)

(-) 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:351
 aligned with Q3IZQ3_RHOS4 | Q3IZQ3 from UniProtKB/TrEMBL  Length:355

    Alignment length:351
                                    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 ETIPVFDGHNDFLLRLLRNPANRETIWLKGDGTGHLDLPRMKEGGFAGGFFAIYVPSPQAHDAAHFEAMMDAPPFELPLPPMIRAEQAQPVALAMAGHLLWMERAARGRFKVCRTAAEVRSCHADGIVSGIMHMEGAEAIGADLDALHLFHSLGLRSLGPVWSRPTVFGHGVPFRFPGSPDTGEGLTEAGRRLVAECNRLKIMLDLSHLNEKGFDDVARLSDAPLVATHSNAHAVTPSTRNLTDRQLAMIRESRGMVGLNFATSFLREDGRRSAEMGWEPVLRHLDHLIDRLGEDHVGMGSDFDGATIPQGIADVTGLPALQAAMRAHGYDEPLMRKLCHENWYGLLERSW 353
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhhhh..hhhhhhhh.......hhhhhhhhheeeeeeee.........hhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhh.eeeeeeee........hhhhhhhhhhheeeee...............ee..........hhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhh....ee...............hhhhhhhhhhh..eeee..hhhhhh..........hhhhhhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ly0 A   3 DTIPVFDGHNDFLLRLLRNPANRETIWLKGDGTGHLDLPRMKEGGFAGGFFAIYVPSPQAHDAAHFEAMMDAPPFELPLPPMIRAEQAQPVALAMAGHLLWMERAARGRFKVCRTAAEVRSCHADGIVSGIMHMEGAEAIGADLDALHLFHSLGLRSLGPVWSRPTVFGHGVPFRFPGSPDTGEGLTEAGRRLVAECNRLKIMLDLSHLNEKGFDDVARLSDAPLVATHSNAHAVTPSTRNLTDRQLAMIRESRGMVGLNFATSFLREDGRRSAEMGWEPVLRHLDHLIDRLGEDHVGMGSDFDGATIPQGIADVTGLPALQAAMRAHGYDEPLMRKLCHENWYGLLERTW 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 


Chain B from PDB  Type:PROTEIN  Length:352
 aligned with Q3IZQ3_RHOS4 | Q3IZQ3 from UniProtKB/TrEMBL  Length:355

    Alignment length:352
                                    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 ETIPVFDGHNDFLLRLLRNPANRETIWLKGDGTGHLDLPRMKEGGFAGGFFAIYVPSPQAHDAAHFEAMMDAPPFELPLPPMIRAEQAQPVALAMAGHLLWMERAARGRFKVCRTAAEVRSCHADGIVSGIMHMEGAEAIGADLDALHLFHSLGLRSLGPVWSRPTVFGHGVPFRFPGSPDTGEGLTEAGRRLVAECNRLKIMLDLSHLNEKGFDDVARLSDAPLVATHSNAHAVTPSTRNLTDRQLAMIRESRGMVGLNFATSFLREDGRRSAEMGWEPVLRHLDHLIDRLGEDHVGMGSDFDGATIPQGIADVTGLPALQAAMRAHGYDEPLMRKLCHENWYGLLERSWG 354
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Peptidase_M19-3ly0B01 B:4-351                                                                                                                                                                                                                                                                                                                               --- Pfam domains (1)
           Pfam domains (2) -Peptidase_M19-3ly0B02 B:4-351                                                                                                                                                                                                                                                                                                                               --- Pfam domains (2)
         Sec.struct. author ....eeeeeehhhhhhhhh..hhhhhhhh.......hhhhhhhhheeeeeeeee........hhhhhhhhh...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
                 3ly0 B   3 DTIPVFDGHNDFLLRLLRNPANRETIWLKGDGTGHLDLPRMKEGGFAGGFFAIYVPSPQAHDAAHFEAMMDAPPFELPLPPMIRAEQAQPVALAMAGHLLWMERAARGRFKVCRTAAEVRSCHADGIVSGIMHMEGAEAIGADLDALHLFHSLGLRSLGPVWSRPTVFGHGVPFRFPGSPDTGEGLTEAGRRLVAECNRLKIMLDLSHLNEKGFDDVARLSDAPLVATHSNAHAVTPSTRNLTDRQLAMIRESRGMVGLNFATSFLREDGRRSAEMGWEPVLRHLDHLIDRLGEDHVGMGSDFDGATIPQGIADVTGLPALQAAMRAHGYDEPLMRKLCHENWYGLLERTWG 354
                                    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
   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 3LY0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LY0)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (4, 4)

Asymmetric 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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