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(-) Description

Title :  CRYSTAL STRUCTURE OF DIPEPTIDASE FROM STREPTOMYCES COELICOLOR COMPLEXED WITH PHOSPHINATE PSEUDODIPEPTIDE L-LEU-D-ALA
 
Authors :  A. A. Fedorov, E. V. Fedorov, J. Cummings, F. M. Raushel, S. C. Almo
Date :  16 May 11  (Deposition) - 22 Jun 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  (Beta-Alpha)8 Barel, Dipeptidase, Phosphinate Pseudodipeptide, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, J. Cummings, F. M. Raushel, S. C. Almo
Crystal Structure Of Dipeptidase From Streptomyces Coelicolor Complexed With Phosphinate Pseudodipeptide L-Leu-D-Ala
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPEPTIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SCO3058, SCBAC19G2.13C
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 1902

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2L3A1Ligand/Ion(2R)-3-[(R)-[(1R)-1-AMINO-3-METHYLBUTYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC ACID
3ZN2Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:20 , ASP A:22 , TRP A:25 , TYR A:68 , GLU A:123 , HIS A:150 , HIS A:191 , HIS A:212 , ARG A:223 , PHE A:248 , ASP A:320 , GLY A:323 , ZN A:402 , ZN A:403 , HOH A:735 , HOH A:911BINDING SITE FOR RESIDUE L3A A 401
2AC2SOFTWAREHIS A:20 , ASP A:22 , GLU A:123 , L3A A:401 , ZN A:403BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREGLU A:123 , HIS A:191 , HIS A:212 , L3A A:401 , ZN A:402BINDING SITE FOR RESIDUE ZN A 403
4AC4SOFTWAREHIS A:126 , ASN A:130 , ASN A:154 , ALA A:155 , HOH A:569 , HOH A:705BINDING SITE FOR RESIDUE EDO A 404
5AC5SOFTWAREVAL A:218 , VAL A:249 , LEU A:250 , GLN A:251 , ASP A:301 , HOH A:520BINDING SITE FOR RESIDUE EDO A 405
6AC6SOFTWAREPHE A:14 , SER A:352 , ALA A:355 , LYS A:360 , ASP A:367 , ARG A:374 , HOH A:601 , HOH A:647BINDING SITE FOR RESIDUE EDO A 406
7AC7SOFTWAREHIS A:49 , ASP A:322 , THR A:324 , PRO A:325 , HOH A:428 , HOH A:714BINDING SITE FOR RESIDUE EDO A 407
8AC8SOFTWARESER A:45 , HIS A:47 , HIS A:49 , HOH A:641 , HOH A:878BINDING SITE FOR RESIDUE EDO A 408
9AC9SOFTWARETYR A:68 , ARG A:70 , SER A:71 , ASP A:72 , HIS A:150 , ASN A:151 , ASP A:152BINDING SITE FOR RESIDUE EDO A 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S2J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S2J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S2J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S2J)

(-) Exons   (0, 0)

(no "Exon" information available for 3S2J)

(-) 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:393
 aligned with Q93J45_STRCO | Q93J45 from UniProtKB/TrEMBL  Length:400

    Alignment length:393
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390   
         Q93J45_STRCO     1 MTSLEKARELLREFPVVDGHNDLPWALREQVRYDLDARDIAADQSAHLHTDLARLRSGGVGAQYWSVYVRSDLPGAVTATLEQIDCVRRLIDRHPGELRAALTAADMEAARAEGRIASLMGAEGGHSIDNSLATLRALYALGVRYMTLTHNDNNAWADSATDEPGVGGLSAFGREVVREMNREGMLVDLSHVAATTMRDALDTSTAPVIFSHSSSRAVCDHPRNIPDDVLERLSANGGMAMVTFVPKFVLQAAVDWTAEADDNMRAHGFHHLDSSPEAMKVHAAFEERVPRPVATVSTVADHLDHMREVAGVDHLGIGGDYDGTPFTPDGLGDVSGYPNLIAELLDRGWSQSDLAKLTWKNAVRVLDAAEDVSRGLRAARGPSNATIEQLDGT 393
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------Peptidase_M19-3s2jA01 A:9-368                                                                                                                                                                                                                                                                                                                                           ------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeeeeehhhhhhhhhhh.hhhhhh...........hhhhhhhhheeeeeee........hhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhh.eeeeeeee.hhhhh.hhhhhhhhhhh.eeeee......................hhhhhhhhhhhhhhh.eee....hhhhhhhhhhhh....ee...............hhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eee...............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s2j A   1 MTSLEKARELLREFPVVDGHNDLPWALREQVRYDLDARDIAADQSAHLHTDLARLRSGGVGAQYWSVYVRSDLPGAVTATLEQIDCVRRLIDRHPGELRAALTAADMEAARAEGRIASLMGAEGGHSIDNSLATLRALYALGVRYMTLTHNDNNAWADSATDEPGVGGLSAFGREVVREMNREGMLVDLSHVAATTMRDALDTSTAPVIFSHSSSRAVCDHPRNIPDDVLERLSANGGMAMVTFVPKFVLQAAVDWTAEADDNMRAHGFHHLDSSPEAMKVHAAFEERVPRPVATVSTVADHLDHMREVAGVDHLGIGGDYDGTPFTPDGLGDVSGYPNLIAELLDRGWSQSDLAKLTWKNAVRVLDAAEDVSRGLRAARGPSNATIEQLDGT 393
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390
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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  (0, 0)

(no "SCOP Domain" information available for 3S2J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S2J)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q93J45_STRCO | Q93J45)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q93J45_STRCO | Q93J45: 3id7 3isi 3itc 3k5x 3s2l 3s2m 3s2n

(-) Related Entries Specified in the PDB File

3k5x THE SAME PROTEIN COMPLEXED WITH ANOTHER INHIBITOR
3s2l
3s2m
3s2n