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Title :   CRYSTAL STRUCTURE OF ENOLASE PRK14017 (TARGET EFI-500653) FROM RALSTONIA PICKETTII 12J WITH MAGNESIUM BOUND

Authors :   Y. Patskovsky, U. A. Ramagopal, B. Hillerich, R. D. Seidel, W. D. Zenche R. Toro, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Function Initiat

Date :   29 Apr 11 (Deposition) - 11 May 11 (Release) - 11 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Enolase, Magnesium Binding Site, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Patskovsky, U. A. Ramagopal, B. Hillerich, R. D. Seidel, W. D. Zencheck, R. Toro, H. J. Imker, J. A. Gerlt, S. C. Almo
Crystal Structure Of Enolase Prk14017 From Ralstonia Pickettii
To Be Published
PubMed: search

Molecule 1 - PUTATIVE D-GALACTONATE DEHYDRATASE
	Chains	:	A, B
	EC Number	:	4.2.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DGOD, RPIC_2990
	Organism Scientific	:	RALSTONIA PICKETTII
	Organism Taxid	:	402626
	Strain	:	12J
	Synonym	:	GALD

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:76 , ILE A:78 , LEU A:79 , CL B:405	BINDING SITE FOR RESIDUE CL A 405
2	AC2	SOFTWARE	ASP A:183 , GLU A:209 , GLU A:235 , HOH A:462 , HOH A:463	BINDING SITE FOR RESIDUE MG A 406
3	AC3	SOFTWARE	CL A:405 , GLY B:75 , GLY B:76 , ILE B:78 , LEU B:79	BINDING SITE FOR RESIDUE CL B 405
4	AC4	SOFTWARE	LYS B:144 , ASP B:183 , GLU B:209 , GLU B:235 , HOH B:480 , HOH B:481	BINDING SITE FOR RESIDUE MG B 406

Asymmetric Unit

No.	Residues
1	B:286	-	B:296

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_1	PS00908	Mandelate racemase / muconate lactonizing enzyme family signature 1.	DGOD_RALPJ	82-107	2	A:82-107 B:82-107
2	MR_MLE_2	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.	DGOD_RALPJ	180-211	2	A:180-211 B:180-211

Biological Unit 1 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_1	PS00908	Mandelate racemase / muconate lactonizing enzyme family signature 1.	DGOD_RALPJ	82-107	8	A:82-107 B:82-107
2	MR_MLE_2	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.	DGOD_RALPJ	180-211	8	A:180-211 B:180-211

(no "Exon" information available for 3RRA)

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:374
 aligned with DGOD_RALPJ | B2UCA8 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:385
                                                                                                                                                                                                                                                                                                                                                                                                                       382   
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380 |   
           DGOD_RALPJ     1 MKITRLTTYRLPPRWMFLKVETDEGVTGWGEPVIEGRARTVEAAVHELSDYLIGQDPSRINDLWQTMYRAGFYRGGPILMSAIAGIDQALWDIKGKVLGVPVYELLGGLVRDKMRTYSWVGGDRPADVIAGMKALQAGGFDHFKLNGCEEMGIIDTSRAVDAAVARVAEIRSAFGNTVEFGLDFHGRVSAPMAKVLIKELEPYRPLFIEEPVLAEQAETYARLAAHTHLPIAAGERMFSRFDFKRVLEAGGVSILQPDLSHAGGITECVKIAAMAEAYDVALAPHCPLGPIALAACLHVDFVSWNATLQEQSMGIHYNKGAELLDYVRNKADFALEGGYIRPPRLPGLGVDIDEALVIERSKEAPDWRNPVWRHADGSVAEW---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...eeeeeeee.....eee......hhhhhhhhhhhhhhhh......hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......eeeeee....hhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhhhhhhheeeee........hhhhhhhhhhhhh...ee.......hhhhhhhhh.....eee.....hhhhhhhhhhhh...ee.......hhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhh.......eee..--------.......hhhhh.ee..ee............hhhhhhhhhh...---................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------MR_MLE_1  PDB: A:82-107   ------------------------------------------------------------------------MR_MLE_2  PDB: A:180-211        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rra A   1 VKITRLTTYRLPPRWMFLKVETDEGVTGWGEPVIEGRARTVEAAVHELSDYLIGQDPSRINDLWQTMYRAGFYRGGPILMSAIAGIDQALWDIKGKVLGVPVYELLGGLVRDKMRTYSWVGGDRPADVIAGMKALQAGGFDHFKLNGCEEMGIIDTSRAVDAAVARVAEIRSAFGNTVEFGLDFHGRVSAPMAKVLIKELEPYRPLFIEEPVLAEQAETYARLAAHTHLPIAAGERMFSRFDFKRVLEAGGVSILQPDLSHAGGITECVKIAAMAEAYDVALAPHCPLGPIALAACLHVDFVSWNATLQEQSM--------ELLDYVRNKADFALEGGYIRPPRLPGLGVDIDEALVIERSKEAP---NPVWRHADGSVAEWAEN 385
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  |      - |     330       340       350       360    |  370       380     
                                                                                                                                                                                                                                                                                                                                                  313      322                                        365 369

Chain B from PDB  Type:PROTEIN  Length:379
 aligned with DGOD_RALPJ | B2UCA8 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:387
                             1                                                                                                                                                                                                                                                                                                                                                                                          382    
                             |       9        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  |    
           DGOD_RALPJ     - -MKITRLTTYRLPPRWMFLKVETDEGVTGWGEPVIEGRARTVEAAVHELSDYLIGQDPSRINDLWQTMYRAGFYRGGPILMSAIAGIDQALWDIKGKVLGVPVYELLGGLVRDKMRTYSWVGGDRPADVIAGMKALQAGGFDHFKLNGCEEMGIIDTSRAVDAAVARVAEIRSAFGNTVEFGLDFHGRVSAPMAKVLIKELEPYRPLFIEEPVLAEQAETYARLAAHTHLPIAAGERMFSRFDFKRVLEAGGVSILQPDLSHAGGITECVKIAAMAEAYDVALAPHCPLGPIALAACLHVDFVSWNATLQEQSMGIHYNKGAELLDYVRNKADFALEGGYIRPPRLPGLGVDIDEALVIERSKEAPDWRNPVWRHADGSVAEW----   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----MR_MLE_N-3rraB01 B:5-107                                                                               ------------------------------------------------------------------------------------------------------------------------------MR_MLE_C-3rraB03 B:234-351                                                                                            ---------------  ------------------ Pfam domains (1)
           Pfam domains (2) -----MR_MLE_N-3rraB02 B:5-107                                                                               ------------------------------------------------------------------------------------------------------------------------------MR_MLE_C-3rraB04 B:234-351                                                                                            ---------------  ------------------ Pfam domains (2)
         Sec.struct. author ...eeeeeeeee...eeeeeeee....eeee......hhhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.......eeeeee....hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhhhhhheeeee........hhhhhhhhhhhhh...ee.......hhhhhhhhh.....eee.....hhhhhhhhhhhh...ee.......hhhhhhhhhhhhhh....ee......hhhhhhhhhhhhh.......eee...------.hhhhh..hhhhh.ee..ee............hhhhhhhhhh....--.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------MR_MLE_1  PDB: B:82-107   ------------------------------------------------------------------------MR_MLE_2  PDB: B:180-211        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rra B   0 MVKITRLTTYRLPPRWMFLKVETDEGVTGWGEPVIEGRARTVEAAVHELSDYLIGQDPSRINDLWQTMYRAGFYRGGPILMSAIAGIDQALWDIKGKVLGVPVYELLGGLVRDKMRTYSWVGGDRPADVIAGMKALQAGGFDHFKLNGCEEMGIIDTSRAVDAAVARVAEIRSAFGNTVEFGLDFHGRVSAPMAKVLIKELEPYRPLFIEEPVLAEQAETYARLAAHTHLPIAAGERMFSRFDFKRVLEAGGVSILQPDLSHAGGITECVKIAAMAEAYDVALAPHCPLGPIALAACLHVDFVSWNATLQEQSMG------AELLDYVRNKADFALEGGYIRPPRLPGLGVDIDEALVIERSKEAPD--NPVWRHADGSVAEWAENL 386
                                     9        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    |    - |     329       339       349       359      |369       379       
                                                                                                                                                                                                                                                                                                                                                    314    321                                          366  |                 
                                                                                                                                                                                                                                                                                                                                                                                                           369

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 3RRA)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Enolase_N (69)

Family: MR_MLE_N (47)

Ralstonia pickettii (strain 12J) (2)

1a	MR_MLE_N-3rraB01	B:5-107
1b	MR_MLE_N-3rraB02	B:5-107

Clan: Enolase_TIM (82)

Family: MR_MLE_C (29)

Ralstonia pickettii (strain 12J) (3)

2a	MR_MLE_C-3rraB03	B:234-351
2b	MR_MLE_C-3rraB04	B:234-351

Asymmetric Unit(hide GO term definitions)

Chain A,B (DGOD_RALPJ | B2UCA8)

molecular function
	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:0008869	galactonate dehydratase activity	Catalysis of the reaction: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H(2)O.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0034194	D-galactonate catabolic process	The chemical reactions and pathways resulting in the breakdown of D-galactonate, the anion of D-galactonic acid.
	GO:0009063	cellular amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown 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.

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3rr1	ENOLASE PRK14017 WITH NO METAL BOUND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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