3CXO - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH MG AND 3-DEOXY-L-RHAMNONATE

Authors :   A. A. Fedorov, E. V. Fedorov, J. F. Rakus, B. K. Hubbard, J. A. Gerlt, S. C. Almo

Date :   24 Apr 08 (Deposition) - 23 Sep 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (4x)

Keywords :   L-Rhamnonate Dehydratase, Enolase Superfamily, 3-Deoxy-L- Rhamnonate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. F. Rakus, A. A. Fedorov, E. V. Fedorov, M. E. Glasner, B. K. Hubbard, J. D. Delli, P. C. Babbitt, S. C. Almo, J. A. Gerlt
Evolution Of Enzymatic Activities In The Enolase Superfamily: L-Rhamnonate Dehydratase.
Biochemistry V. 47 9944 2008
PubMed-ID: 18754693 | Reference-DOI: 10.1021/BI800914R
(for further references see the PDB file header)

Molecule 1 - PUTATIVE GALACTONATE DEHYDRATASE
	Atcc	:	700720
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Gene	:	YFAW, STM2291
	Organism Scientific	:	SALMONELLA TYPHIMURIUM LT2
	Organism Taxid	:	99287
	Strain	:	LT2, SGSC1412

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	1N5	1	Ligand/Ion	(2R,4S)-2,4,7-TRIHYDROXYHEPTANOIC ACID
2	3LR	1	Ligand/Ion	3,6-DIDEOXY-L-ARABINO-HEXONIC ACID
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	1N5	1	Ligand/Ion	(2R,4S)-2,4,7-TRIHYDROXYHEPTANOIC ACID
2	3LR	1	Ligand/Ion	3,6-DIDEOXY-L-ARABINO-HEXONIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	1N5	4	Ligand/Ion	(2R,4S)-2,4,7-TRIHYDROXYHEPTANOIC ACID
2	3LR	4	Ligand/Ion	3,6-DIDEOXY-L-ARABINO-HEXONIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:33 , TRP A:40 , ILE A:45 , ARG A:59 , LYS A:189 , ASP A:226 , TRP A:228 , GLU A:252 , GLU A:280 , HIS A:329 , GLU A:349 , LEU A:351	BINDING SITE FOR RESIDUE 3LR A 501
2	AC2	SOFTWARE	ASP A:226 , GLU A:252 , GLU A:280	BINDING SITE FOR RESIDUE MG A 500
3	AC3	SOFTWARE	ASP B:226 , GLU B:252 , GLU B:280	BINDING SITE FOR RESIDUE MG B 500
4	AC4	SOFTWARE	HIS B:33 , ILE B:45 , ARG B:59 , LYS B:189 , PRO B:191 , ASP B:226 , TRP B:228 , GLU B:252 , GLU B:280 , HIS B:329 , GLU B:349 , LEU B:351	BINDING SITE FOR RESIDUE 1N5 B 502

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

Asymmetric Unit

No.	Residues
1	Asp A:365	-	Pro A:366
2	Asp B:365	-	Pro B:366

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_1	PS00908	Mandelate racemase / muconate lactonizing enzyme family signature 1.	RHMD_SALTY	136-161	2	A:136-161 B:136-161

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_1	PS00908	Mandelate racemase / muconate lactonizing enzyme family signature 1.	RHMD_SALTY	136-161	2	A:136-161 B:136-161

Biological Unit 2 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_1	PS00908	Mandelate racemase / muconate lactonizing enzyme family signature 1.	RHMD_SALTY	136-161	8	A:136-161 B:136-161

(no "Exon" information available for 3CXO)

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:402
 aligned with RHMD_SALTY | Q8ZNF9 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:402
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403  
           RHMD_SALTY     4 IMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeee....................hhhhh........hhhhh..hhhhh.....eeeeeeee....eeeeeeehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeee..hhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeee.....hhhhhhhhhh....ee........hhhhhhhhhhhhhhh..ee....hhhhhhhhhh.......eeee................ee........eee.hhhh......ee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------MR_MLE_1  PDB: A:136-161  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cxo A   4 IMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403

Chain B from PDB  Type:PROTEIN  Length:402
 aligned with RHMD_SALTY | Q8ZNF9 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:402
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403  
           RHMD_SALTY     4 IMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeee....................hhhhh........hhhhh..hhhhh.....eeeeeeee....eeeeeeehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeee..hhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeee.....hhhhhhhhhh....ee........hhhhhhhhhhhhhhh..ee....hhhhhhhhhh.......eeee................ee........eee.hhhh......ee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------MR_MLE_1  PDB: B:136-161  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cxo B   4 IMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH 405
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403

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 3CXO)

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

(no "Pfam Domain" information available for 3CXO)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RHMD_SALTY | Q8ZNF9)

molecular function
	GO:0050032	L-rhamnonate dehydratase activity	Catalysis of the reaction: L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H(2)O.
	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: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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		Asp A:365 - Pro A:366	[ RasMol ]
		Asp B:365 - Pro B:366	[ RasMol ]

Biological Units
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3box	THE SAME PROTEIN WITHOUT BOUND LIGAND

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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