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(-) Description

Title :  CRYSTAL STRUCTURE OF DIPEPTIDASE FROM STREPTOMICS COELICOLOR COMPLEXED WITH PHOSPHINATE PSEUDODIPEPTIDE L-ALA-D-ASP AT 1.4A RESOLUTION.
 
Authors :  A. A. Fedorov, E. V. Fedorov, J. Cummings, F. M. Raushel, S. C. Almo
Date :  08 Oct 09  (Deposition) - 12 Jan 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Dipeptidase From Streptomics Coelicolor, The Closest Bacterial Homolog To Human Renal Dipeptidase, Phosphinate Pseudodipeptide, L-Ala-D-Asp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Cummings, T. T. Nguyen, A. A. Fedorov, P. Kolb, C. Xu, E. V. Fedorov, B. K. Shoichet, D. P. Barondeau, S. C. Almo, F. M. Raushel
Structure, Mechanism, And Substrate Profile For Sco3058: The Closest Bacterial Homologue To Human Renal Dipeptidase .
Biochemistry V. 49 611 2010
PubMed-ID: 20000809  |  Reference-DOI: 10.1021/BI901935Y

(-) 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 Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1P8D1Ligand/IonPHOSPHINATE PSEUDODIPEPTIDE L-ALA-D-ASP
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1P8D1Ligand/IonPHOSPHINATE PSEUDODIPEPTIDE L-ALA-D-ASP
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1P8D2Ligand/IonPHOSPHINATE PSEUDODIPEPTIDE L-ALA-D-ASP
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:20 , ASP A:22 , 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 , THR A:324 , ZN A:402 , ZN A:403 , HOH A:573 , HOH A:585 , HOH A:614 , HOH A:640 , HOH A:667 , HOH A:756BINDING SITE FOR RESIDUE P8D A 401
2AC2SOFTWAREHIS A:20 , ASP A:22 , GLU A:123BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREGLU A:123 , HIS A:191 , HIS A:212BINDING SITE FOR RESIDUE ZN A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K5X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K5X)

(-) Exons   (0, 0)

(no "Exon" information available for 3K5X)

(-) 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:391
 aligned with Q93J45_STRCO | Q93J45 from UniProtKB/TrEMBL  Length:400

    Alignment length:391
                                    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 MTSLEKARELLREFPVVDGHNDLPWALREQVRYDLDARDIAADQSAHLHTDLARLRSGGVGAQYWSVYVRSDLPGAVTATLEQIDCVRRLIDRHPGELRAALTAADMEAARAEGRIASLMGAEGGHSIDNSLATLRALYALGVRYMTLTHNDNNAWADSATDEPGVGGLSAFGREVVREMNREGMLVDLSHVAATTMRDALDTSTAPVIFSHSSSRAVCDHPRNIPDDVLERLSANGGMAMVTFVPKFVLQAAVDWTAEADDNMRAHGFHHLDSSPEAMKVHAAFEERVPRPVATVSTVADHLDHMREVAGVDHLGIGGDYDGTPFTPDGLGDVSGYPNLIAELLDRGWSQSDLAKLTWKNAVRVLDAAEDVSRGLRAARGPSNATIEQLD 391
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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..................hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k5x A   1 MTSLEKARELLREFPVVDGHNDLPWALREQVRYDLDARDIAADQSAHLHTDLARLRSGGVGAQYWSVYVRSDLPGAVTATLEQIDCVRRLIDRHPGELRAALTAADMEAARAEGRIASLMGAEGGHSIDNSLATLRALYALGVRYMTLTHNDNNAWADSATDEPGVGGLSAFGREVVREMNREGMLVDLSHVAATTMRDALDTSTAPVIFSHSSSRAVCDHPRNIPDDVLERLSANGGMAMVTFVPKFVLQAAVDWTAEADDNMRAHGFHHLDSSPEAMKVHAAFEERVPRPVATVSTVADHLDHMREVAGVDHLGIGGDYDGTPFTPDGLGDVSGYPNLIAELLDRGWSQSDLAKLTWKNAVRVLDAAEDVSRGLRAARGPSNATIEQLD 391
                                    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 3K5X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K5X)

(-) Gene Ontology  (3, 3)

Asymmetric 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

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UniProtKB/TrEMBL
        Q93J45_STRCO | Q93J45: 3id7 3isi 3itc 3s2j 3s2l 3s2m 3s2n

(-) Related Entries Specified in the PDB File

3id7 THE SAME PROTEIN IN APO FORM