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(-) Description

Title :  CRYSTAL STRUCTURE OF SCO3058 WITH BOUND CITRATE AND GLYCEROL
 
Authors :  T. T. Nguyen, J. A. Cummings, C. -L. Tsai, D. P. Barondeau, F. M. Raushel
Date :  28 Aug 09  (Deposition) - 02 Feb 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim-Barrel Hydrolase (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 - RENAL 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, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2GOL1Ligand/IonGLYCEROL
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:20 , ASP A:22 , GLU A:123 , ZN A:502 , GOL A:504 , HOH A:505BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREGLU A:123 , HIS A:191 , HIS A:212 , ZN A:501 , CIT A:503 , HOH A:505BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREHIS A:150 , ASN A:151 , HIS A:191 , HIS A:212 , ARG A:223 , LYS A:247 , PHE A:248 , ASP A:320 , GLY A:323 , THR A:324 , ZN A:502 , GOL A:504 , HOH A:505 , HOH A:541 , HOH A:764 , HOH A:779 , HOH A:781 , HOH A:887 , HOH A:902BINDING SITE FOR RESIDUE CIT A 503
4AC4SOFTWAREASP A:22 , TYR A:68 , GLU A:123 , GLY A:323 , ZN A:501 , CIT A:503 , HOH A:505 , HOH A:764 , HOH A:887 , HOH A:903BINDING SITE FOR RESIDUE GOL A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ITC)

(-) 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:392
 aligned with Q93J45_STRCO | Q93J45 from UniProtKB/TrEMBL  Length:400

    Alignment length:392
                                    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 MTSLEKARELLREFPVVDGHNDLPWALREQVRYDLDARDIAADQSAHLHTDLARLRSGGVGAQYWSVYVRSDLPGAVTATLEQIDCVRRLIDRHPGELRAALTAADMEAARAEGRIASLMGAEGGHSIDNSLATLRALYALGVRYMTLTHNDNNAWADSATDEPGVGGLSAFGREVVREMNREGMLVDLSHVAATTMRDALDTSTAPVIFSHSSSRAVCDHPRNIPDDVLERLSANGGMAMVTFVPKFVLQAAVDWTAEADDNMRAHGFHHLDSSPEAMKVHAAFEERVPRPVATVSTVADHLDHMREVAGVDHLGIGGDYDGTPFTPDGLGDVSGYPNLIAELLDRGWSQSDLAKLTWKNAVRVLDAAEDVSRGLRAARGPSNATIEQLDG 392
               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...............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3itc A   1 MTSLEKARELLREFPVVDGHNDLPWALREQVRYDLDARDIAADQSAHLHTDLARLRSGGVGAQYWSVYVRSDLPGAVTATLEQIDCVRRLIDRHPGELRAALTAADMEAARAEGRIASLMGAEGGHSIDNSLATLRALYALGVRYMTLTHNDNNAWADSATDEPGVGGLSAFGREVVREMNREGMLVDLSHVAATTMRDALDTSTAPVIFSHSSSRAVCDHPRNIPDDVLERLSANGGMAMVTFVPKFVLQAAVDWTAEADDNMRAHGFHHLDSSPEAMKVHAAFEERVPRPVATVSTVADHLDHMREVAGVDHLGIGGDYDGTPFTPDGLGDVSGYPNLIAELLDRGWSQSDLAKLTWKNAVRVLDAAEDVSRGLRAARGPSNATIEQLDG 392
                                    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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  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 3ITC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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        Q93J45_STRCO | Q93J45: 3id7 3isi 3k5x 3s2j 3s2l 3s2m 3s2n

(-) Related Entries Specified in the PDB File

3isi CRYSTAL STRUCTURE OF SCO3058 WITH BOUND INHIBITOR L-ALA-L- ASP PHOSPHINODIPEPTIDE