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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE 4-AMINO-4-DEOXYCHORISMATE LYASE (HS_0128) FROM HAEMOPHILUS SOMNUS 129PT AT 2.40 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  28 Feb 08  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  D-Aminoacid Aminotransferase-Like Plp-Dependent Enzymes Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of D-Aminoacid Aminotransferase-Like Plp-Dependent Enzyme (Yp_718332. 1) From Haemophilus Somnus 129Pt At 2. 40 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D-AMINOACID AMINOTRANSFERASE-LIKE PLP-DEPENDENT ENZYME
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_718332.1, HS_0128
    Organism Scientific: HAEMOPHILUS SOMNUS
    Organism Taxid: 205914
    Strain: 129PT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3MSE4Mod. Amino AcidSELENOMETHIONINE
4SO45Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:35 , HIS A:52 , ASN A:70 , HIS A:71 , TYR A:74 , LEU A:76 , HOH A:214BINDING SITE FOR RESIDUE SO4 A 194
2AC2SOFTWAREASN A:19 , ILE A:20 , SER A:21 , TYR A:22 , HOH A:227 , HOH A:261BINDING SITE FOR RESIDUE SO4 A 195
3AC3SOFTWAREHIS A:58 , ARG A:59 , GLU A:60BINDING SITE FOR RESIDUE SO4 A 196
4AC4SOFTWARECYS A:94 , ASP A:95 , HIS A:96BINDING SITE FOR RESIDUE SO4 A 197
5AC5SOFTWAREARG A:106 , ASN A:110 , HOH A:218 , HOH A:240BINDING SITE FOR RESIDUE SO4 A 198
6AC6SOFTWARELYS A:84 , TYR A:86 , ARG A:185 , LEU A:186 , ASN A:191BINDING SITE FOR RESIDUE GOL A 199

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 3CEB)

(-) 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:194
 aligned with Q0I0Z6_HAES1 | Q0I0Z6 from UniProtKB/TrEMBL  Length:193

    Alignment length:194
                             1                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189    
         Q0I0Z6_HAES1     - -MWQFPLFETILIEQGQAKNISYHQQRYEKSLLKFYPKMKLQPFDLAKIIAKHTALFTHREGLIRCRIDYNHHDYVLQCFPYQQKVYRTFKPVFCDHIDYSLKFSDRTLLNNLLKQKEECDEIMIIRQGKVTDCSIGNLIFRQNNQWITPDKPLLEGTQRAKLLEQKKIIAREIFFEDLAQYEEIRLINAMNGL 193
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cebA01 A:0-84  [code=3.30.470.10, no name defined]                                  3cebA02 A:85-193 D-amino Acid Aminotransferase, subunit A, domain 2                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee..ee.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.......eeeee............hhhhhhhhhhhh...eeeeee..ee......eeeeee..eeeee......hhhhhhhhhh...eee..hhhhhhhh..eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ceb A   0 GmWQFPLFETILIEQGQAKNISYHQQRYEKSLLKFYPKmKLQPFDLAKIIAKHTALFTHREGLIRCRIDYNHHDYVLQCFPYQQKVYRTFKPVFCDHIDYSLkFSDRTLLNNLLKQKEECDEImIIRQGKVTDCSIGNLIFRQNNQWITPDKPLLEGTQRAKLLEQKKIIAREIFFEDLAQYEEIRLINAmNGL 193
                             |       9        19        29        39        49        59        69        79        89        99  |    109       119   |   129       139       149       159       169       179       189|   
                             |                                   38-MSE                                                         102-LLP              123-MSE                                                            190-MSE
                             1-MSE
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q0I0Z6_HAES1 | Q0I0Z6)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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