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(-) Description

Title :  X-RAY STRUCTURE OF THE TRYPTOPHAN LYASE NOSL WITH TRYPTOPHAN, 5'-DEOXYADENOSINE AND METHIONINE BOUND
 
Authors :  Y. Nicolet, L. Zeppieri, P. Amara, J. -C. Fontecilla-Camps
Date :  14 Aug 14  (Deposition) - 17 Sep 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Radical Sam Enzyme/Beta-Alpha Barrel, Tryptophan Lyase, Fe4S4 Cluster And S-Adenosyl-L-Methionine, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Nicolet, L. Zeppieri, P. Amara, J. C. Fontecilla-Camps
Crystal Structure Of Tryptophan Lyase (Nosl): Evidence For Radical Formation At The Amino Group Of Tryptophan.
Angew. Chem. Int. Ed. Engl. V. 53 11840 2014
PubMed-ID: 25196319  |  Reference-DOI: 10.1002/ANIE.201407320

(-) Compounds

Molecule 1 - NOSL
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: PLASMIDE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMIDE
    Gene: NOSL
    Organism Scientific: STREPTOMYCES ACTUOSUS
    Organism Taxid: 1885
    Strain: STREPTOMYCES ACTUOSUS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 24)

Asymmetric Unit (9, 24)
No.NameCountTypeFull Name
15AD2Ligand/Ion5'-DEOXYADENOSINE
2BR7Ligand/IonBROMIDE ION
3GOL4Ligand/IonGLYCEROL
4MET2Mod. Amino AcidMETHIONINE
5NA2Ligand/IonSODIUM ION
6SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
7SF42Ligand/IonIRON/SULFUR CLUSTER
8TRP2Mod. Amino AcidTRYPTOPHAN
9ZN1Ligand/IonZINC ION
Biological Unit 1 (6, 12)
No.NameCountTypeFull Name
15AD2Ligand/Ion5'-DEOXYADENOSINE
2BR-1Ligand/IonBROMIDE ION
3GOL2Ligand/IonGLYCEROL
4MET2Mod. Amino AcidMETHIONINE
5NA-1Ligand/IonSODIUM ION
6SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
7SF42Ligand/IonIRON/SULFUR CLUSTER
8TRP2Mod. Amino AcidTRYPTOPHAN
9ZN-1Ligand/IonZINC ION
Biological Unit 2 (6, 16)
No.NameCountTypeFull Name
15AD2Ligand/Ion5'-DEOXYADENOSINE
2BR-1Ligand/IonBROMIDE ION
3GOL6Ligand/IonGLYCEROL
4MET2Mod. Amino AcidMETHIONINE
5NA-1Ligand/IonSODIUM ION
6SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
7SF42Ligand/IonIRON/SULFUR CLUSTER
8TRP2Mod. Amino AcidTRYPTOPHAN
9ZN-1Ligand/IonZINC ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:141 , GLY A:142 , GLU A:143 , ASN A:175 , GLY A:177 , LYS A:224 , ARG A:230 , GLN A:363 , 5AD A:502 , SAH A:503 , SF4 A:504 , HOH A:642BINDING SITE FOR RESIDUE MET A 501
02AC2SOFTWAREMET A:101 , PHE A:202 , GLU A:204 , ARG A:286 , ALA A:288 , ARG A:323 , GLN A:363 , PHE A:364 , MET A:501 , SAH A:503 , TRP A:505 , HOH A:643BINDING SITE FOR RESIDUE 5AD A 502
03AC3SOFTWARETYR A:90 , MET A:101 , THR A:141 , GLY A:142 , ASN A:175 , GLY A:177 , PHE A:202 , GLU A:204 , LYS A:224 , ARG A:230 , ARG A:286 , ALA A:288 , ARG A:323 , GLN A:363 , PHE A:364 , MET A:501 , 5AD A:502 , SF4 A:504 , HOH A:642 , HOH A:643BINDING SITE FOR RESIDUE SAH A 503
04AC4SOFTWARECYS A:95 , CYS A:99 , CYS A:102 , MET A:104 , ARG A:105 , LYS A:224 , MET A:501 , SAH A:503BINDING SITE FOR RESIDUE SF4 A 504
05AC5SOFTWAREPRO A:88 , TYR A:90 , PHE A:202 , THR A:321 , THR A:322 , ARG A:323 , SER A:340 , GLY A:342 , 5AD A:502 , HOH A:610 , HOH A:612 , HOH A:649BINDING SITE FOR RESIDUE TRP A 505
06AC6SOFTWAREHIS A:84 , ARG A:171 , TYR A:173 , THR A:198 , ASP A:279 , HOH A:625 , HOH A:750BINDING SITE FOR RESIDUE GOL A 506
07AC7SOFTWAREARG A:286 , LYS A:290BINDING SITE FOR RESIDUE BR A 507
08AC8SOFTWAREARG A:292 , HIS A:388 , HOH A:699BINDING SITE FOR RESIDUE BR A 508
09AC9SOFTWAREARG A:82 , HOH A:627BINDING SITE FOR RESIDUE BR A 509
10BC1SOFTWAREGLU A:380 , VAL A:386 , PHE A:389 , HOH A:629 , HOH A:635BINDING SITE FOR RESIDUE NA A 510
11BC2SOFTWARETHR B:141 , GLY B:142 , GLU B:143 , ASN B:175 , GLY B:177 , LYS B:224 , ARG B:230 , GLN B:363 , 5AD B:502 , SAH B:503 , SF4 B:504 , HOH B:616BINDING SITE FOR RESIDUE MET B 501
12BC3SOFTWAREMET B:101 , PHE B:202 , GLU B:204 , LEU B:250 , ARG B:284 , MET B:285 , ARG B:286 , ALA B:288 , ARG B:323 , GLN B:363 , PHE B:364 , MET B:501 , SAH B:503 , TRP B:505 , HOH B:610BINDING SITE FOR RESIDUE 5AD B 502
13BC4SOFTWAREMET B:101 , THR B:141 , GLY B:142 , GLU B:143 , ASN B:175 , PHE B:202 , GLU B:204 , LYS B:224 , ARG B:230 , ARG B:284 , MET B:285 , ARG B:286 , ALA B:288 , ARG B:323 , GLN B:363 , PHE B:364 , MET B:501 , 5AD B:502 , SF4 B:504 , HOH B:610 , HOH B:616BINDING SITE FOR RESIDUE SAH B 503
14BC5SOFTWARECYS B:95 , CYS B:99 , CYS B:102 , MET B:104 , ARG B:105 , LYS B:224 , MET B:501 , SAH B:503BINDING SITE FOR RESIDUE SF4 B 504
15BC6SOFTWAREPRO B:88 , TYR B:90 , PHE B:202 , THR B:321 , THR B:322 , ARG B:323 , SER B:340 , GLY B:342 , PHE B:364 , 5AD B:502 , HOH B:606 , HOH B:611 , HOH B:633BINDING SITE FOR RESIDUE TRP B 505
16BC7SOFTWAREHIS B:84 , ARG B:171 , TYR B:173 , THR B:198 , ASP B:279 , ARG B:317 , HOH B:646 , HOH B:798 , HOH B:826BINDING SITE FOR RESIDUE GOL B 506
17BC8SOFTWAREHIS B:130 , HIS B:131 , ARG B:373 , HOH B:684 , HOH B:773 , HOH B:992BINDING SITE FOR RESIDUE GOL B 507
18BC9SOFTWARETHR B:210 , ARG B:213 , PHE B:214 , LEU B:253 , HIS B:254 , ASP B:255 , ARG B:292 , HOH B:810 , HOH B:898BINDING SITE FOR RESIDUE GOL B 508
19CC1SOFTWAREARG B:82 , HOH B:697BINDING SITE FOR RESIDUE BR B 509
20CC2SOFTWAREARG B:292 , HIS B:388 , HOH B:764 , HOH B:925BINDING SITE FOR RESIDUE BR B 510
21CC3SOFTWARELEU B:167 , ZN B:513BINDING SITE FOR RESIDUE BR B 511
22CC4SOFTWAREGLU B:380 , VAL B:386 , PHE B:389 , HOH B:654BINDING SITE FOR RESIDUE NA B 512
23CC5SOFTWAREGLU B:126 , HIS B:130 , BR B:511 , HOH B:931BINDING SITE FOR RESIDUE ZN B 513
24CC6SOFTWAREARG B:286 , PRO B:287 , LYS B:290 , HOH B:829BINDING SITE FOR RESIDUE BR B 514

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R34)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:80 -Pro A:81
2Arg B:80 -Pro B:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R34)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R34)

(-) Exons   (0, 0)

(no "Exon" information available for 4R34)

(-) 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh..hhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhh......eee.eeee..........................hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh.......eeeeeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhh..ee.ee................hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh.eee..............................hhhhhhhhhhhh...ee.....hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r34 A  15 GDFVLPELEDVRAEAATVDTRAVLALAEGEEPAESRAAVALALWEDRSIGTAELQAAAEARCGARRPRLHTFVPLYTTNYCDSECKMCSMRKGNHRLDRKFSGRKEITEQLEILYHHEGVRGVGFLTGEYEDKHTRLASAFRIGWAIRTALDLGFERVYFNIGSMEQDEIDVLGEWIGREDPVTMCVFQESYDRETYRRFMGKTSVGVPKADFDRRVVSFDRWLDAGYRYVNPGVLVGLHDDLSAELVSLVAHGDHLRSRGATADLSVPRMRPAMKSRDTTRVGDDDYLRLMSVVAFTCPEQRLVLTTREPQEFQDVALGLAGVISPGSPDVAPYRAGCEARNDEKSSQFLVADLRRPRHILGRIEASGTPVDHFVNPAGEASRMW 505
                                    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   |||
                                                                                                                                                                                                                                                                                                                                                                                                                         398||
                                                                                                                                                                                                                                                                                                                                                                                                                          501|
                                                                                                                                                                                                                                                                                                                                                                                                                           505


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhh..hhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhhhhh......ee.eeee..........................hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh.......eeee......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhh..ee.ee................hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh.eee..............................hhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r34 B  10 SHAMTGDFVLPELEDVRAEAATVDTRAVLALAEGEEPAESRAAVALALWEDRSIGTAELQAAAEARCGARRPRLHTFVPLYTTNYCDSECKMCSMRKGNHRLDRKFSGRKEITEQLEILYHHEGVRGVGFLTGEYEDKHTRLASAFRIGWAIRTALDLGFERVYFNIGSMEQDEIDVLGEWIGREDPVTMCVFQESYDRETYRRFMGKTSVGVPKADFDRRVVSFDRWLDAGYRYVNPGVLVGLHDDLSAELVSLVAHGDHLRSRGATADLSVPRMRPAMKSRDTTRVGDDDYLRLMSVVAFTCPEQRLVLTTREPQEFQDVALGLAGVISPGSPDVAPYRAGCEARNDEKSSQFLVADLRRPRHILGRIEASGTPVDHFVNPAMW 505
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389   |||
                                                                                                                                                                                                                                                                                                                                                                                                                         393||
                                                                                                                                                                                                                                                                                                                                                                                                                          501|
                                                                                                                                                                                                                                                                                                                                                                                                                           505
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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 4R34)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R34)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R34)

(-) Gene Ontology  (4, 4)

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4r33