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(-) Description

Title :  CRYSTAL STRUCTURE OF THE APO FORM OF Y74F MUTANT E. COLI TRYPTOPHANASE
 
Authors :  A. Kogan, G. Y. Gdalevsky, R. Cohen-Luria, Y. Goldgur, A. H. Parola, O. A
Date :  28 May 07  (Deposition) - 10 Jun 08  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Lyase, Pyridoxal Phosphate, Tryptophan Catabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Kogan, G. Y. Gdalevsky, R. Cohen-Luria, Y. Goldgur, R. S. Phillips, A. H. Parola, O. Almog
Conformational Changes And Loose Packing Promote E. Coli Tryptophanase Cold Lability.
Bmc Struct. Biol. V. 9 65 2009
PubMed-ID: 19814824  |  Reference-DOI: 10.1186/1472-6807-9-65

(-) Compounds

Molecule 1 - TRYPTHOPANASE
    ChainsA
    EC Number4.1.99.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 5-471
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymL-TRYPTOPHAN INDOLE-LYASE, TNASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CME8Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:65 , ARG A:69 , HOH A:2132BINDING SITE FOR RESIDUE CL A 1472
2AC2SOFTWAREHOH A:2056 , HOH A:2120 , HOH A:2148 , HOH A:2150 , HOH A:2399 , HOH A:2435BINDING SITE FOR RESIDUE MG A 1473

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V1P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:195 -Thr A:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V1P)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_ELIM_LYASEPS00853 Beta-eliminating lyases pyridoxal-phosphate attachment site.TNAA_ECOLI260-278  1A:260-278
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_ELIM_LYASEPS00853 Beta-eliminating lyases pyridoxal-phosphate attachment site.TNAA_ECOLI260-278  4A:260-278

(-) Exons   (0, 0)

(no "Exon" information available for 2V1P)

(-) 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:467
 aligned with TNAA_ECOLI | P0A853 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:467
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       
           TNAA_ECOLI     5 KHLPEPFRIRVIEPVKRTTRAYREEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAYSGSRSYYALAESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFDTGVRYDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQREAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFFDVYTECRTLCVVQEGFPTYGGLEGGAMERLAVGLYDGMNLDWLAYRIAQVQYLVDGLEEIGVVCQQAGGHAAFVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEIGSFLLGRDPKTGKQLPCPAELLRLTIPRATYTQTHMDFIIEAFKHVKENAANIKGLTFTYEPKVLRHFTAKLKEV 471
               SCOP domains d2v1pa1 A:5-471 Tryptophan indol-lyase (tryptophanase)                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2v1pA01 A:5-60,A:327-471                                2v1pA02 A:61-326 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                      2v1pA01 A:5-60,A:327-471 Aspartate Aminotransferase, domain 1                                                                                     CATH domains
               Pfam domains --------------------------------------------Beta_elim_lyase-2v1pA01 A:49-438                                                                                                                                                                                                                                                                                                                                                                      --------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhh..hhhhhhhhhh.ee..........hhhhhhhh.........hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhh..eeee...................hhhhhhhhhhhhhhhhh..eeee...hhhhh...hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.eeeee..........eeeee.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeee....eeeehhhhh...hhhhhhhhhhhhhhhhhhhee.eeehhhhhh..............eeee.......hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhheeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------BETA_ELIM_LYASE    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v1p A   5 KHLPEPFRIRVIEPVKRTTRAYREEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAFSGSRSYYALAESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFDTGVRYDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQREAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFFDVYTECRTLcVVQEGFPTYGGLEGGAMERLAVGLYDGMNLDWLAYRIAQVQYLVDGLEEIGVVcQQAGGHAAFVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEIGSFLLGRDPKTGKQLPCPAELLRLTIPRATYTQTHMDFIIEAFKHVKENAANIKGLTFTYEPKVLRHFTAKLKEV 471
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294   |   304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       
                                                                                                                                                                                                                                                                                                                               298-CME                                               352-CME                                                                                                                   

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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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (TNAA_ECOLI | P0A853)
molecular function
    GO:0080146    L-cysteine desulfhydrase activity    Catalysis of the reaction: L-cysteine + H2O = ammonia + pyruvate + hydrogen sulfide + H+.
    GO:0016830    carbon-carbon lyase activity    Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    GO:0030955    potassium ion binding    Interacting selectively and non-covalently with potassium (K+) ions.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0009034    tryptophanase activity    Catalysis of the reaction: L-tryptophan + H(2)O = indole + NH(4)(+) + pyruvate.
biological process
    GO:0009072    aromatic amino acid family metabolic process    The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0006569    tryptophan catabolic process    The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
    GO:0006568    tryptophan metabolic process    The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
cellular component
    GO:0060187    cell pole    Either of two different areas at opposite ends of an axis of a cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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        TNAA_ECOLI | P0A8532c44 2oqx 2v0y 4up2 4w1y 4w4h 5d8g

(-) Related Entries Specified in the PDB File

2c44 CRYSTAL STRUCTURE OF E. COLI TRYPTOPHANASE
2v0y CRYSTAL STRUCTURE OF APO C298S TRYPTOPHANASE FROM E.COLI