2PV7 - JenaLib

Title :   CRYSTAL STRUCTURE OF CHORISMATE MUTASE / PREPHENATE DEHYDROGENASE (TYRA) (1574749) FROM HAEMOPHILUS INFLUENZAE RD AT 2.00 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   09 May 07 (Deposition) - 22 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   1574749, Chorismate Mutase Type Ii, Chorismate Mutase / Prephenate Dehydrogenase (Tyra), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Isomerase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. J. Chiu, P. Abdubek, T. Astakhova, H. L. Axelrod, D. Carlton, T. Clayton, D. Das, M. C. Deller, L. Duan, J. Feuerhelm, J. C. Grant, A. Grzechnik, G. W. Han, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, P. Kozbial, S. S. Krishna, A. Kumar, D. Marciano, D. Mcmullan, M. D. Miller, A. T. Morse, E. Nigoghossian, L. Okach, R. Reyes, H. J. Tien, C. B. Trame, H. Van Den Bedem, D. Weekes, Q. Xu, K. O. Hodgson, J. Wooley, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
The Structure Of Haemophilus Influenzae Prephenate Dehydrogenase Suggests Unique Features Of Bifunctional Tyra Enzymes.
Acta Crystallogr. , Sect. F V. 66 1317 2010
PubMed-ID: 20944228 | Reference-DOI: 10.1107/S1744309110021688

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:179 , HIS A:200 , PRO A:201 , PHE A:203 , GLN A:256 , HIS A:260 , ARG A:297 , GLN A:301 , TYR A:306 , ILE A:309 , NAD A:400 , HOH A:412 , HOH A:460 , TYR B:288	BINDING SITE FOR RESIDUE TYR A 401
2	AC2	SOFTWARE	TYR A:288 , HOH A:408 , SER B:179 , HIS B:200 , PRO B:201 , PHE B:203 , GLN B:256 , HIS B:260 , ARG B:297 , GLN B:301 , TYR B:306 , NAD B:400 , HOH B:427 , HOH B:580	BINDING SITE FOR RESIDUE TYR B 401
3	AC3	SOFTWARE	GLY A:107 , TYR A:109 , GLY A:110 , LYS A:111 , LEU A:112 , LEU A:130 , ASP A:131 , ARG A:132 , TRP A:135 , SER A:151 , VAL A:152 , PRO A:153 , ILE A:154 , LEU A:156 , LEU A:177 , THR A:178 , SER A:179 , PRO A:201 , PHE A:203 , GLY A:204 , LEU A:305 , TYR A:401 , HOH A:427 , HOH A:433 , HOH A:435 , HOH A:462 , HOH A:488 , HOH A:489 , HOH A:535 , HOH A:539 , HOH A:557	BINDING SITE FOR RESIDUE NAD A 400
4	AC4	SOFTWARE	GLY B:107 , TYR B:109 , GLY B:110 , LYS B:111 , LEU B:112 , LEU B:130 , ASP B:131 , ARG B:132 , TRP B:135 , VAL B:152 , PRO B:153 , ILE B:154 , LEU B:156 , LEU B:177 , THR B:178 , SER B:179 , PRO B:201 , PHE B:203 , GLY B:204 , LEU B:305 , TYR B:401 , HOH B:406 , HOH B:413 , HOH B:417 , HOH B:425 , HOH B:436 , HOH B:462 , HOH B:568 , HOH B:571 , HOH B:592 , HOH B:601	BINDING SITE FOR RESIDUE NAD B 400

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

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:277
 aligned with TYRA_HAEIN | P43902 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:282
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371  
           TYRA_HAEIN    92 GFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQAND 373
               SCOP domains d2pv7a2 A:92-243 Prephenate dehydrogenase TyrA                                                                                                          d2pv7a1 A:244-371 Prephenate dehydrogenase TyrA                                                                                  - SCOP domains
               CATH domains 2pv7A01 A:92-250 NAD(P)-binding Rossmann-like Domain                                                                                                           2pv7A02 A:251-371 6-phosphogluconate dehydrogenase C-terminal     like domain                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeee...hhhhhhhhhhhhh....eeee...hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeeeee............eeeeeeeehhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhh----hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------PDH_ADH  PDB: A:101-364 UniProt: 101-364                                                                                                                                                                                                                                --------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pv7 A  92 GFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENmLLADLTSVKREPLAKmLEVHTGAVLGLHPmFGADIASmAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNmTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAmIGRLFAQDAELYADIIm----NLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQA-Y 401
                                   101       111       121       131       141       151       161       171|      181      |191       201|      211       221       231       241       251|      261       271       281       291  |    301       311    |  321       331       341       351       361       371 |
                                                                                                          172-MSE         188-MSE       202-MSE 210-MSE                                   252-MSE                                   294-MSE          311-MSE6                                                    371 |
                                                                                                                                                                                                                                                                                                                   401

Chain B from PDB  Type:PROTEIN  Length:281
 aligned with TYRA_HAEIN | P43902 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:281
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371 
           TYRA_HAEIN    92 GFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQAN 372
               SCOP domains d2pv7b2 B:92-243 Prephenate dehydrogenase TyrA                                                                                                          d2pv7b1 B:244-371 Prephenate dehydrogenase TyrA                                                                                 - SCOP domains
               CATH domains 2pv7B01 B:92-250 NAD(P)-binding Rossmann-like Domain                                                                                                           2pv7B02 B:251-371 6-phosphogluconate dehydrogenase C-terminal like domain                                                - CATH domains
           Pfam domains (1) ------------------------------------PDH-2pv7B01 B:128-348                                                                                                                                                                                                        ------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------PDH-2pv7B02 B:128-348                                                                                                                                                                                                        ------------------------ Pfam domains (2)
         Sec.struct. author ...........eeee...hhhhhhhhhhhhhh...eeee...hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeeeee............eeeeeeeehhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PDH_ADH  PDB: B:101-364 UniProt: 101-364                                                                                                                                                                                                                                -------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pv7 B  92 GFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENmLLADLTSVKREPLAKmLEVHTGAVLGLHPmFGADIASmAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNmTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAmIGRLFAQDAELYADIImDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQAY 401
                                   101       111       121       131       141       151       161       171|      181      |191       201|      211       221       231       241       251|      261       271       281       291  |    301       311       321       331       341       351       361       371|
                                                                                                          172-MSE         188-MSE       202-MSE 210-MSE                                   252-MSE                                   294-MSE          311-MSE                                                     371|
                                                                                                                                                                                                                                                                                                                  401

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 (2, 4)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TYRA_HAEIN | P43902)

molecular function
	GO:0070403	NAD+ binding	Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	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:0004106	chorismate mutase activity	Catalysis of the reaction: chorismate = prephenate.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0008977	prephenate dehydrogenase (NAD+) activity	Catalysis of the reaction: NAD(+) + prephenate = (4-hydroxyphenyl)pyruvate + CO(2) + NADH.
	GO:0004665	prephenate dehydrogenase (NADP+) activity	Catalysis of the reaction: NADP(+) + prephenate = (4-hydroxyphenyl)pyruvate + CO(2) + NADPH.
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:0046417	chorismate metabolic process	The chemical reactions and pathways involving chorismate, the anion of (3R-trans)-3-((1-carboxyethenyl)oxy)-4-hydroxy-1,5-cyclohexadiene-1-carboxylic acid.
	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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006571	tyrosine biosynthetic process	The chemical reactions and pathways resulting in the formation of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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