3NYZ - JenaLib

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Title :   CRYSTAL STRUCTURE OF KEMP ELIMINATION CATALYST 1A53-2

Authors :   T. M. Lee, H. K. Privett, J. T. Kaiser, S. L. Mayo

Date :   15 Jul 10 (Deposition) - 29 Jun 11 (Release) - 25 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.51

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Tim Barrel, Kemp Elimination Enzyme, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. K. Privett, G. Kiss, T. M. Lee, R. Blomberg, R. A. Chica, L. M. Thomas, D. Hilvert, K. N. Houk, S. L. Mayo
Iterative Approach To Computational Enzyme Design.
Proc. Natl. Acad. Sci. Usa V. 109 3790 2012
PubMed-ID: 22357762 | Reference-DOI: 10.1073/PNAS.1118082108

Molecule 1 - INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
	Chains	:	A, B
	EC Number	:	4.1.1.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, TRPC
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Synonym	:	IGPS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:53 , ARG A:182 , GLN A:211 , GLY A:212 , GLY A:233 , SER A:234 , HOH A:273 , HOH A:274 , HOH A:275 , HOH A:276 , HOH A:277	BINDING SITE FOR RESIDUE SO4 A 262
2	AC2	SOFTWARE	LYS B:53 , GLN B:211 , GLY B:212 , GLY B:233 , SER B:234 , HOH B:290 , HOH B:291 , HOH B:292 , HOH B:326 , HOH B:334 , HOH B:343	BINDING SITE FOR RESIDUE SO4 B 262

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IGPS	PS00614	Indole-3-glycerol phosphate synthase signature.	TRPC_SULSO	48-62	2	A:48-62 B:48-62

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IGPS	PS00614	Indole-3-glycerol phosphate synthase signature.	TRPC_SULSO	48-62	1	A:48-62 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IGPS	PS00614	Indole-3-glycerol phosphate synthase signature.	TRPC_SULSO	48-62	1	- B:48-62

(no "Exon" information available for 3NYZ)

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:247
 aligned with TRPC_SULSO | Q06121 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           TRPC_SULSO     2 PRYLKGWLKDVVQLSLRRPSFRASRQRPIISLNERILEFNKRNITAIIAEYKRKSPSGLDVERDPIEYSKFMERYAVGLSILTEEKYFNGSYETLRKIASSVSIPILMKDFIVKESQIDDAYNLGADTVLLIVKILTERELESLLEYARSYGMEPLIEINDENDLDIALRIGARFIGINSRDLETLEINKENQRKLISMIPSNVVKVAESGISERNEIEELRKLGVNAFLIGSSLMRNPEKIKEFIL 248
               SCOP domains d3nyza_ A: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.eee........hhhhhhhhhhhhh...eeeee............hhhhhhhhhhh...eeeee.hhhhhh.hhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh.....eeee.hhhhhhhhhhh...eeeee.........hhhhhhhhhhhh....eeeee....hhhhhhhhhh....eeeehhhhhhh.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------IGPS           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nyz A   2 PRYLKGWLKDVVQLSLRRPSFRASRQRPIISLNERILEFNKRNITAIIAAYKRKSPSGLDVERDPIEYSKFMERYAVGLAIATEEKYFNGSYETLRKIASSVSIPILMWDFIVKESQIDDAYNLGADTVALIVKILTERELESLLEYARSYGMEPAIVINDENDLDIALRIGARFIEIASRDLETLEINKENQRKLISMIPSNVVKVAWQGISERNEIEELRKLGVNAFGIGSSLMRNPEKIKEFIL 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with TRPC_SULSO | Q06121 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           TRPC_SULSO     2 PRYLKGWLKDVVQLSLRRPSFRASRQRPIISLNERILEFNKRNITAIIAEYKRKSPSGLDVERDPIEYSKFMERYAVGLSILTEEKYFNGSYETLRKIASSVSIPILMKDFIVKESQIDDAYNLGADTVLLIVKILTERELESLLEYARSYGMEPLIEINDENDLDIALRIGARFIGINSRDLETLEINKENQRKLISMIPSNVVKVAESGISERNEIEELRKLGVNAFLIGSSLMRNPEKIKEFIL 248
               SCOP domains d3nyzb_ B: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) IGPS-3nyzB01 B:2-247                                                                                                                                                                                                                                  - Pfam domains (1)
           Pfam domains (2) IGPS-3nyzB02 B:2-247                                                                                                                                                                                                                                  - Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhh..eee........hhhhhhhhhhhh....eeeee............hhhhhhhhhhh...eeeee........hhhhhhhhhh.....eeee....hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeee.........hhhhhhhhhh......eeeee....hhhhhhhhhh....eeeehhhhhhh.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------IGPS           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nyz B   2 PRYLKGWLKDVVQLSLRRPSFRASRQRPIISLNERILEFNKRNITAIIAAYKRKSPSGLDVERDPIEYSKFMERYAVGLAIATEEKYFNGSYETLRKIASSVSIPILMWDFIVKESQIDDAYNLGADTVALIVKILTERELESLLEYARSYGMEPAIVINDENDLDIALRIGARFIEIASRDLETLEINKENQRKLISMIPSNVVKVAWQGISERNEIEELRKLGVNAFGIGSSLMRNPEKIKEFIL 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: Tryptophan biosynthesis enzymes (108)

Protein domain: automated matches (30)

Sulfolobus solfataricus [TaxId: 2287] (6)

1a	d3nyza_	A:
1b	d3nyzb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: IGPS (10)

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (6)

1a	IGPS-3nyzB01	B:2-247
1b	IGPS-3nyzB02	B:2-247

Asymmetric Unit(hide GO term definitions)

Chain A,B (TRPC_SULSO | Q06121)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0004425	indole-3-glycerol-phosphate synthase activity	Catalysis of the reaction: 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = 1-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O.
	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:0004640	phosphoribosylanthranilate isomerase activity	Catalysis of the reaction: N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate.
biological process
	GO:0009073	aromatic amino acid family biosynthetic process	The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	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.
	GO:0000162	tryptophan biosynthetic process	The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
	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.

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