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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE 4-AMINO-4-DEOXYCHORISMATE LYASE. (YP_094631.1) FROM LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. PHILADELPHIA 1 AT 1.78 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  17 Feb 10  (Deposition) - 02 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative 4-Amino-4-Deoxychorismate Lyase. , Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Lyase, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative 4-Amino-4-Deoxychorismate Lyase. (Yp_094631. 1) From Legionella Pneumophila Subsp. Pneumophila Str. Philadelphia 1 At 1. 78 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 4-AMINO-4-DEOXYCHORISMATE LYASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LPG0595
    Organism Scientific: LEGIONELLA PNEUMOPHILA
    Organism Taxid: 272624
    Strain: PHILADELPHIA 1 / ATCC 33152 / DSM 7513

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3MSE8Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:161 , LEU A:234 , ARG A:242 , HOH A:356 , HOH A:399BINDING SITE FOR RESIDUE EDO A 272
2AC2SOFTWAREGLN A:210 , MSE A:214 , VAL A:216 , HOH A:470 , HOH A:586BINDING SITE FOR RESIDUE EDO A 273
3AC3SOFTWARETYR A:114 , SER A:115 , HOH A:484 , HOH B:532BINDING SITE FOR RESIDUE EDO A 274
4AC4SOFTWAREMSE B:44 , PRO B:198 , HOH B:319 , HOH B:406BINDING SITE FOR RESIDUE EDO B 272
5AC5SOFTWAREPHE B:112 , ASN B:113 , TYR B:114 , SER B:115BINDING SITE FOR RESIDUE PO4 B 273

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LUL)

(-) 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:268
 aligned with Q5ZXY5_LEGPH | Q5ZXY5 from UniProtKB/TrEMBL  Length:271

    Alignment length:270
                                    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
         Q5ZXY5_LEGPH     1 MPTRVIEDKGDMTPSFGIDDRIFLGEGLFETIRVNSSKPSFAYMHWERLGNSARQLGIPFEISFDDWFEHLIQKIQKDNLYHGGIKAILSGGPASRGLAERGQVSQLIFQTFNYSIQKHPVRLISINWLRDKANPLYQLKSVNYLEAIIAQRQAIAVGADDALFFNTENHVTETTCANLFLIENNILYTPRVEDGILPGITRARLISHCQQHKMSVQEISLTKKRIEDADAVFLTNSLQGIRRVLSLDNIIFEVNHPIIDKLIFLLNQDE 270
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....--........hhhhhh.eeeeeeeee..ee.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....eeeeeeee..............eeeeeeee........eeeeeeeeee...hhhhhh....hhhhhhhhhhhhhh...eeeeee....eeee...eeeeee..eeee.hhhhh...hhhhhhhhhhhhhh...eee...hhhhhhh..eeeeee...eeeeeeee..ee....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lul A   1 mPTRVIEDK--mTPSFGIDDRIFLGEGLFETIRVNSSKPSFAYmHWERLGNSARQLGIPFEISFDDWFEHLIQKIQKDNLYHGGIKAILSGGPASRGLAERGQVSQLIFQTFNYSIQKHPVRLISINWLRDKANPLYQLkSVNYLEAIIAQRQAIAVGADDALFFNTENHVTETTCANLFLIENNILYTPRVEDGILPGITRARLISHCQQHKmSVQEISLTKKRIEDADAVFLTNSLQGIRRVLSLDNIIFEVNHPIIDKLIFLLNQDE 270
                            |       |- |      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
                            |       9  |                              44-MSE                                                                                         140-LLP                                                                   214-MSE                                                    
                            1-MSE     12-MSE                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:269
 aligned with Q5ZXY5_LEGPH | Q5ZXY5 from UniProtKB/TrEMBL  Length:271

    Alignment length:271
                                    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 
         Q5ZXY5_LEGPH     1 MPTRVIEDKGDMTPSFGIDDRIFLGEGLFETIRVNSSKPSFAYMHWERLGNSARQLGIPFEISFDDWFEHLIQKIQKDNLYHGGIKAILSGGPASRGLAERGQVSQLIFQTFNYSIQKHPVRLISINWLRDKANPLYQLKSVNYLEAIIAQRQAIAVGADDALFFNTENHVTETTCANLFLIENNILYTPRVEDGILPGITRARLISHCQQHKMSVQEISLTKKRIEDADAVFLTNSLQGIRRVLSLDNIIFEVNHPIIDKLIFLLNQDES 271
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------Aminotran_4-3lulB01 B:40-266                                                                                                                                                                                                       ----- Pfam domains (1)
           Pfam domains (2) ---------------------------------------Aminotran_4-3lulB02 B:40-266                                                                                                                                                                                                       ----- Pfam domains (2)
         Sec.struct. author ..eee....--........hhhhhh.eeeeeeeee..ee.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....eeeeeeee..............eeeeeeee........eeeeeeeeee...hhhhhh....hhhhhhhhhhhhhh...eeeeee....eeee...eeeeee..eeee.hhhhh...hhhhhhhhhhhhhh...eee...hhhhhhh..eeeeee...eeeeeeee..ee....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lul B   1 mPTRVIEDK--mTPSFGIDDRIFLGEGLFETIRVNSSKPSFAYmHWERLGNSARQLGIPFEISFDDWFEHLIQKIQKDNLYHGGIKAILSGGPASRGLAERGQVSQLIFQTFNYSIQKHPVRLISINWLRDKANPLYQLkSVNYLEAIIAQRQAIAVGADDALFFNTENHVTETTCANLFLIENNILYTPRVEDGILPGITRARLISHCQQHKmSVQEISLTKKRIEDADAVFLTNSLQGIRRVLSLDNIIFEVNHPIIDKLIFLLNQDES 271
                            |       |- |      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 
                            1-MSE   9  |                              44-MSE                                                                                         140-LLP                                                                   214-MSE                                                     
                                      12-MSE
   Legend:   → Mismatch (orange background)
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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 3LUL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Aminotran_4] (8)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5ZXY5_LEGPH | Q5ZXY5)
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.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
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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