3NZ1 - JenaLib

Title :   CRYSTAL STRUCTURE OF KEMP ELIMINATION CATALYST 1A53-2 COMPLEXED WITH TRANSITION STATE ANALOG 5-NITRO BENZOTRIAZOLE

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 :   1.56

Chains :   Asym./Biol. Unit : A

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

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:51 , LYS A:53 , ALA A:81 , ALA A:83 , TRP A:110 , GLU A:178 , TRP A:210 , GLN A:211 , SO4 A:267	BINDING SITE FOR RESIDUE 3NY A 262
02	AC2	SOFTWARE	ARG A:3 , TYR A:4 , ARG A:97	BINDING SITE FOR RESIDUE SO4 A 263
03	AC3	SOFTWARE	ARG A:36 , GLU A:39 , LYS A:42 , ARG A:43	BINDING SITE FOR RESIDUE SO4 A 264
04	AC4	SOFTWARE	LYS A:53 , TRP A:210 , GLN A:211 , GLY A:212 , GLY A:233 , SER A:234 , SO4 A:267 , HOH A:325 , HOH A:357 , HOH A:363 , HOH A:384	BINDING SITE FOR RESIDUE SO4 A 265
05	AC5	SOFTWARE	LYS A:10 , ARG A:18 , LYS A:71	BINDING SITE FOR RESIDUE SO4 A 266
06	AC6	SOFTWARE	LYS A:53 , SER A:56 , SER A:58 , PHE A:89 , GLN A:211 , 3NY A:262 , SO4 A:265 , HOH A:363 , HOH A:414 , HOH A:431	BINDING SITE FOR RESIDUE SO4 A 267
07	AC7	SOFTWARE	SER A:21 , ARG A:23 , ARG A:64 , ASP A:65 , GLU A:68 , HOH A:293 , HOH A:361	BINDING SITE FOR RESIDUE SO4 A 268
08	AC8	SOFTWARE	PHE A:40 , ILE A:45 , ARG A:75 , ILE A:247	BINDING SITE FOR RESIDUE TLA A 269
09	AC9	SOFTWARE	TYR A:148 , SER A:151 , TYR A:152	BINDING SITE FOR RESIDUE TLA A 270
10	BC1	SOFTWARE	TRP A:8 , LEU A:187 , ASN A:204 , HOH A:324 , HOH A:333 , HOH A:397	BINDING SITE FOR RESIDUE TLA A 271

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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:249
 aligned with TRPC_SULSO | Q06121 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:249
                                                                                                                                                                                                                                                                                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      |  
           TRPC_SULSO     2 PRYLKGWLKDVVQLSLRRPSFRASRQRPIISLNERILEFNKRNITAIIAEYKRKSPSGLDVERDPIEYSKFMERYAVGLSILTEEKYFNGSYETLRKIASSVSIPILMKDFIVKESQIDDAYNLGADTVLLIVKILTERELESLLEYARSYGMEPLIEINDENDLDIALRIGARFIGINSRDLETLEINKENQRKLISMIPSNVVKVAESGISERNEIEELRKLGVNAFLIGSSLMRNPEKIKEFIL--   -
               SCOP domains d3nz1a_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains IGPS-3nz1A01 A:2-247                                                                                                                                                                                                                                  --- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.............hhhhhhhhhhhhh...eeeee............hhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeee.........hhhhhhhhhhh.....eeeee....hhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------IGPS           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nz1 A   2 PRYLKGWLKDVVQLSLRRPSFRASRQRPIISLNERILEFNKRNITAIIAAYKRKSPSGLDVERDPIEYSKFMERYAVGLAIATEEKYFNGSYETLRKIASSVSIPILMWDFIVKESQIDDAYNLGADTVALIVKILTERELESLLEYARSYGMEPAIVINDENDLDIALRIGARFIEIASRDLETLEINKENQRKLISMIPSNVVKVAWQGISERNEIEELRKLGVNAFGIGSSLMRNPEKIKEFILGS 250
                                    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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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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