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(-) Description

Title :  THE STRUCTURE OF A CREATINE_N SUPERFAMILY DOMAIN OF A DIPEPTIDASE FROM STREPTOCOCCUS THERMOPHILUS.
 
Authors :  M. E. Cuff, J. C. Mack, S. Clancy, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  25 Oct 10  (Deposition) - 03 Nov 10  (Release) - 03 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Creatinase_n Domain, Pfam01321, Stu0629, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, J. C. Mack, S. Clancy, A. Joachimiak
The Structure Of A Creatine_n Superfamily Domain Of A Dipeptidase From Streptococcus Thermophilus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPEPTIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Gene: PEPQ, STU0629
    Organism Scientific: STREPTOCOCCUS THERMOPHILUS
    Organism Taxid: 264199
    Strain: LMG 18311

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2MSE3Mod. Amino AcidSELENOMETHIONINE
3NA2Ligand/IonSODIUM ION
4NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:8 , ARG A:50 , PRO A:52 , HOH A:155 , HOH A:156BINDING SITE FOR RESIDUE NHE A 135
02AC2SOFTWAREGLY A:88BINDING SITE FOR RESIDUE EDO A 136
03AC3SOFTWAREARG A:50 , SER A:78 , ALA A:90 , HOH A:197BINDING SITE FOR RESIDUE EDO A 137
04AC4SOFTWAREASN A:103 , ASN A:105 , HOH A:159 , HOH A:160 , HOH A:225BINDING SITE FOR RESIDUE EDO A 138
05AC5SOFTWAREPRO A:24 , ASP A:34 , HOH A:297BINDING SITE FOR RESIDUE EDO A 139
06AC6SOFTWAREGLY A:32 , ASP A:34 , ARG A:63BINDING SITE FOR RESIDUE EDO A 140
07AC7SOFTWARELYS A:86 , LEU A:89 , ALA A:90 , THR A:92 , HOH A:233BINDING SITE FOR RESIDUE EDO A 141
08AC8SOFTWAREMSE A:1 , HIS A:9 , LEU A:59 , GLU A:60 , ARG A:63 , HOH A:152 , HOH A:244BINDING SITE FOR RESIDUE EDO A 142
09AC9SOFTWAREGLN A:113 , GLY A:118 , ARG A:119 , PHE A:120BINDING SITE FOR RESIDUE EDO A 143
10BC1SOFTWAREGLU A:39 , HOH A:182BINDING SITE FOR RESIDUE EDO A 144
11BC2SOFTWARETRP A:82 , THR A:114BINDING SITE FOR RESIDUE EDO A 145
12BC3SOFTWAREGLN A:113 , PHE A:116 , HOH A:203 , HOH A:262 , HOH A:267BINDING SITE FOR RESIDUE NA A 146
13BC4SOFTWARESER A:65 , LEU A:68 , HOH A:278 , HOH A:279 , HOH A:304 , HOH A:305BINDING SITE FOR RESIDUE NA A 147

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PEB)

(-) 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    
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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:132
 aligned with Q5M567_STRT2 | Q5M567 from UniProtKB/TrEMBL  Length:361

    Alignment length:132
                             1                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  
         Q5M567_STRT2     - -MSKLDRIRHFLNENKSGLAIVSDPVTVNYLTGFDCDPHERQMFLFVYENREPALFVPALEVARASSVLDFPVFGYVDSENPWQKIKAGLASTDIPIIYAEFDNLNVTKFQGLQTVFEGRFENLTPFIHKMR 131
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---Creatinase_N-3pebA01 A:3-131                                                                                                      Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeee.hhhhhhhhhh..........eeeee.....eeeee..hhhhhhhhh...eeee....hhhhhhhhhh...eeeeeee.....hhhhhhhhhhhheeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3peb A   0 AmSKLDRIRHFLNENKSGLAIVSDPVTVNYLTGFDCDPHERQmFLFVYENREPALFVPALEVARASSVLDFPVFGYVDSENPWQKIKAGLASTDIPIIYAEFDNLNVTKFQGLQTVFEGRFENLTPFIHKmR 131
                             |       9        19        29        39  |     49        59        69        79        89        99       109       119       129| 
                             |                                       42-MSE                                                                                 130-MSE
                             1-MSE
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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 3PEB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: AMP_N-like (22)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5M567_STRT2 | Q5M567)
molecular function
    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.

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