4R33 - JenaLib

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Title :   X-RAY STRUCTURE OF THE TRYPTOPHAN LYASE NOSL WITH TRYPTOPHAN AND S-ADENOSYL-L-HOMOCYSTEINE 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 :   1.78

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

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 15)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	K	2	Ligand/Ion	POTASSIUM ION
4	NA	1	Ligand/Ion	SODIUM ION
5	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
6	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER
7	TRP	2	Mod. Amino Acid	TRYPTOPHAN

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
6	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER
7	TRP	2	Mod. Amino Acid	TRYPTOPHAN

Biological Unit 2 (4, 12)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	6	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
6	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER
7	TRP	2	Mod. Amino Acid	TRYPTOPHAN

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:101 , THR A:141 , GLY A:142 , ASN A:175 , PHE A:202 , GLU A:204 , LYS A:224 , ARG A:230 , ARG A:286 , ARG A:323 , GLN A:363 , PHE A:364 , SF4 A:502 , HOH A:642 , HOH A:643	BINDING SITE FOR RESIDUE SAH A 501
02	AC2	SOFTWARE	CYS A:95 , CYS A:99 , CYS A:102 , MET A:104 , ARG A:105 , LYS A:224 , SAH A:501	BINDING SITE FOR RESIDUE SF4 A 502
03	AC3	SOFTWARE	PRO A:88 , TYR A:90 , LEU A:140 , PHE A:202 , THR A:321 , THR A:322 , ARG A:323 , SER A:340 , GLY A:342 , PHE A:364 , HOH A:610 , HOH A:612 , HOH A:649	BINDING SITE FOR RESIDUE TRP A 503
04	AC4	SOFTWARE	HIS A:84 , ARG A:171 , TYR A:173 , THR A:198 , ASP A:279 , HOH A:624 , HOH A:764	BINDING SITE FOR RESIDUE GOL A 504
05	AC5	SOFTWARE	GLU A:380 , VAL A:386 , PHE A:389 , HOH A:634	BINDING SITE FOR RESIDUE K A 505
06	AC6	SOFTWARE	MET B:101 , THR B:141 , GLY B:142 , ASN B:175 , PHE B:202 , GLU B:204 , LYS B:224 , ARG B:230 , LEU B:250 , ARG B:284 , MET B:285 , ARG B:286 , ALA B:288 , ARG B:323 , GLN B:363 , PHE B:364 , SF4 B:502 , HOH B:611 , HOH B:617 , HOH B:962	BINDING SITE FOR RESIDUE SAH B 501
07	AC7	SOFTWARE	CYS B:95 , CYS B:99 , CYS B:102 , MET B:104 , ARG B:105 , LYS B:224 , SAH B:501	BINDING SITE FOR RESIDUE SF4 B 502
08	AC8	SOFTWARE	PRO 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 , HOH B:607 , HOH B:612 , HOH B:634	BINDING SITE FOR RESIDUE TRP B 503
09	AC9	SOFTWARE	HIS B:84 , ARG B:171 , TYR B:173 , THR B:198 , ASP B:279 , ARG B:317 , HOH B:647 , HOH B:820 , HOH B:984	BINDING SITE FOR RESIDUE GOL B 504
10	BC1	SOFTWARE	HIS B:130 , HIS B:131 , ARG B:373 , HOH B:1015	BINDING SITE FOR RESIDUE GOL B 505
11	BC2	SOFTWARE	THR B:210 , ARG B:213 , LEU B:253 , HIS B:254 , ASP B:255 , ARG B:292 , HOH B:835 , HOH B:922 , HOH B:963	BINDING SITE FOR RESIDUE GOL B 506
12	BC3	SOFTWARE	GLU B:126 , HIS B:130 , CL B:509	BINDING SITE FOR RESIDUE NA B 507
13	BC4	SOFTWARE	GLU B:380 , VAL B:386 , PHE B:389 , HOH B:655	BINDING SITE FOR RESIDUE K B 508
14	BC5	SOFTWARE	LEU B:167 , NA B:507 , HOH B:854	BINDING SITE FOR RESIDUE CL B 509
15	BC6	SOFTWARE	GLU B:48 , HOH B:1000	BINDING SITE FOR RESIDUE CL B 510

(no "SS Bond" information available for 4R33)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 4R33)

(no "PROSITE Motif" information available for 4R33)

(no "Exon" information available for 4R33)

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
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Chain A from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               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.......eeee......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhh..ee.ee................hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh.eee..............................hhhhhhhhhhhh...ee.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r33 A  15 GDFVLPELEDVRAEAATVDTRAVLALAEGEEPAESRAAVALALWEDRSIGTAELQAAAEARCGARRPRLHTFVPLYTTNYCDSECKMCSMRKGNHRLDRKFSGRKEITEQLEILYHHEGVRGVGFLTGEYEDKHTRLASAFRIGWAIRTALDLGFERVYFNIGSMEQDEIDVLGEWIGREDPVTMCVFQESYDRETYRRFMGKTSVGVPKADFDRRVVSFDRWLDAGYRYVNPGVLVGLHDDLSAELVSLVAHGDHLRSRGATADLSVPRMRPAMKSRDTTRVGDDDYLRLMSVVAFTCPEQRLVLTTREPQEFQDVALGLAGVISPGSPDVAPYRAGCEARNDEKSSQFLVADLRRPRHILGRIEASGTPVDHFVNPAGEASR 398
                                    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

Chain B from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhh..hhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhhhh.......ee.eeee..........................hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh.......eeee......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhh..ee.ee................hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh.eee..............................hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r33 B  10 SHAMTGDFVLPELEDVRAEAATVDTRAVLALAEGEEPAESRAAVALALWEDRSIGTAELQAAAEARCGARRPRLHTFVPLYTTNYCDSECKMCSMRKGNHRLDRKFSGRKEITEQLEILYHHEGVRGVGFLTGEYEDKHTRLASAFRIGWAIRTALDLGFERVYFNIGSMEQDEIDVLGEWIGREDPVTMCVFQESYDRETYRRFMGKTSVGVPKADFDRRVVSFDRWLDAGYRYVNPGVLVGLHDDLSAELVSLVAHGDHLRSRGATADLSVPRMRPAMKSRDTTRVGDDDYLRLMSVVAFTCPEQRLVLTTREPQEFQDVALGLAGVISPGSPDVAPYRAGCEARNDEKSSQFLVADLRRPRHILGRIEASGTPVDHFVNPA 393
                                    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

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4R33)

(no "CATH Domain" information available for 4R33)

(no "Pfam Domain" information available for 4R33)

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	Cis Peptide Bonds
		Arg A:80 - Pro A:81	[ RasMol ]
		Arg B:80 - Pro B:81	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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