3DFH - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PUTATIVE MANDELATE RACEMASE / MUCONATE LACTONIZING ENZYME FROM VIBRIONALES BACTERIUM SWAT-3

Authors :   V. N. Malashkevich, R. Toro, S. R. Wasserman, A. J. Meyer, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)

Date :   12 Jun 08 (Deposition) - 01 Jul 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: C  (8x)
Biol. Unit 2: A,B  (4x)
Biol. Unit 3: A (1x),B (1x)
Biol. Unit 4: C  (2x)
Biol. Unit 5: A,B  (1x)
Biol. Unit 6: C  (2x)

Keywords :   Structural Genomics, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Putative Mandelate Racemase / Muconate Lactonizing Enzyme, Psi-2, New York Sgx Research Center For Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. N. Malashkevich, R. Toro, S. R. Wasserman, A. J. Meyer, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Mandelate Racemase / Muconate Lactonizing Enzyme From Vibrionales Bacterium Swat-3
To Be Published
PubMed: search

Molecule 1 - MANDELATE RACEMASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3(BC)
	Expression System Strain	:	BL21(DE3)CODON+RIL
	Expression System Vector Type	:	PLASMID
	Gene	:	VSWAT3_13707
	Organism Scientific	:	VIBRIONALES BACTERIUM
	Organism Taxid	:	391574
	Strain	:	SWAT-3

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (8x)	:			C
Biological Unit 2 (4x)	:	A	B
Biological Unit 3 (1x)	:	A (1x)	B (1x)
Biological Unit 4 (2x)	:			C
Biological Unit 5 (1x)	:	A	B
Biological Unit 6 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NA	3	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER C:249	BINDING SITE FOR RESIDUE NA C 501
2	AC2	SOFTWARE	SER A:249	BINDING SITE FOR RESIDUE NA A 502
3	AC3	SOFTWARE	SER B:249	BINDING SITE FOR RESIDUE NA B 503

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

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MR_MLE_1	PS00908	Mandelate racemase / muconate lactonizing enzyme family signature 1.	IMAND_VIBBS	89-114	3	A:91-116 B:91-116 C:91-116

Biological Unit 1 (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.	IMAND_VIBBS	89-114	8	- - C:91-116

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.	IMAND_VIBBS	89-114	8	A:91-116 B:91-116 -

Biological Unit 3 (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.	IMAND_VIBBS	89-114	2	A:91-116 B:91-116 -

Biological Unit 4 (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.	IMAND_VIBBS	89-114	2	- - C:91-116

Biological Unit 5 (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.	IMAND_VIBBS	89-114	2	A:91-116 B:91-116 -

Biological Unit 6 (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.	IMAND_VIBBS	89-114	2	- - C:91-116

(no "Exon" information available for 3DFH)

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:359
 aligned with IMAND_VIBBS | A5KUH4 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:379
                             1                                                                                                                                                                                                                                                                                                                                                                                         
                             |       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         
          IMAND_VIBBS     - -MKETIISDIHCIITKPDRHNLITVVVETNEGVTGFGCATFQQRPLAVKTMVDEYLKPILIGKNANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKLAGMPLHQLFGGKSRDAIPVYTHATSDTMEGIYDLVEGFLEKGYKHIRCQLGFYGGVPTDLHTTQNPTEGSYYDQDQYMDNTLTMFKSLREKYGNQFHILHDVHERLFPNQAIQFAKEVEQYKPYFIEDILPPNQTEWLDNIRSQSSVSLGLGELFNNPEEWKSLIANRRIDFIRCHVSQIGGITPALKLGHLCQNFGVRIAWHCPPDMTPIGAAVNTHLNVHLHNAAIQEHVEYNGNTHKVFPNAAEPINGYLYASEIAGIGVEIDREAAAEFP 378
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dfhA01 A:2-110,A:364-380 Enolase-like, N-terminal domain                                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3dfhA01           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee......eeeeeeee.....eeeee....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee..--------------------hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhh.....eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhh.........ee............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------MR_MLE_1  PDB: A:91-116   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dfh A   2 SLKETIISDIHCIITKPDRHNLITVVVETNEGVTGFGCATFQQRPLAVKTMVDEYLKPILIGKNANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKLAGMPLHQLFGGKSRDAIPVYTHATSDTMEGIYDLVEGFLEKGYKHIRCQLGF--------------------DQDQYMDNTLTMFKSLREKYGNQFHILHDVHERLFPNQAIQFAKEVEQYKPYFIEDILPPNQTEWLDNIRSQSSVSLGLGELFNNPEEWKSLIANRRIDFIRCHVSQIGGITPALKLGHLCQNFGVRIAWHCPPDMTPIGAAVNTHLNVHLHNAAIQEHVEYNGNTHKVFPNAAEPINGYLYASEIAGIGVEIDREAAAEFP 380
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      |  -         -       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371         
                                                                                                                                                                                      158                  179

Chain B from PDB  Type:PROTEIN  Length:359
 aligned with IMAND_VIBBS | A5KUH4 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:379
                             1                                                                                                                                                                                                                                                                                                                                                                                         
                             |       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         
          IMAND_VIBBS     - -MKETIISDIHCIITKPDRHNLITVVVETNEGVTGFGCATFQQRPLAVKTMVDEYLKPILIGKNANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKLAGMPLHQLFGGKSRDAIPVYTHATSDTMEGIYDLVEGFLEKGYKHIRCQLGFYGGVPTDLHTTQNPTEGSYYDQDQYMDNTLTMFKSLREKYGNQFHILHDVHERLFPNQAIQFAKEVEQYKPYFIEDILPPNQTEWLDNIRSQSSVSLGLGELFNNPEEWKSLIANRRIDFIRCHVSQIGGITPALKLGHLCQNFGVRIAWHCPPDMTPIGAAVNTHLNVHLHNAAIQEHVEYNGNTHKVFPNAAEPINGYLYASEIAGIGVEIDREAAAEFP 378
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dfhB01 B:2-110,B:364-380 Enolase-like, N-terminal domain                                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3dfhB01           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee......eeeeeeee.....eeeee....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee..--------------------hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhh.....eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhh.........ee............hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------MR_MLE_1  PDB: B:91-116   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dfh B   2 SLKETIISDIHCIITKPDRHNLITVVVETNEGVTGFGCATFQQRPLAVKTMVDEYLKPILIGKNANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKLAGMPLHQLFGGKSRDAIPVYTHATSDTMEGIYDLVEGFLEKGYKHIRCQLGF--------------------DQDQYMDNTLTMFKSLREKYGNQFHILHDVHERLFPNQAIQFAKEVEQYKPYFIEDILPPNQTEWLDNIRSQSSVSLGLGELFNNPEEWKSLIANRRIDFIRCHVSQIGGITPALKLGHLCQNFGVRIAWHCPPDMTPIGAAVNTHLNVHLHNAAIQEHVEYNGNTHKVFPNAAEPINGYLYASEIAGIGVEIDREAAAEFP 380
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      |  -         -       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371         
                                                                                                                                                                                      158                  179

Chain C from PDB  Type:PROTEIN  Length:359
 aligned with IMAND_VIBBS | A5KUH4 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:379
                             1                                                                                                                                                                                                                                                                                                                                                                                         
                             |       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         
          IMAND_VIBBS     - -MKETIISDIHCIITKPDRHNLITVVVETNEGVTGFGCATFQQRPLAVKTMVDEYLKPILIGKNANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKLAGMPLHQLFGGKSRDAIPVYTHATSDTMEGIYDLVEGFLEKGYKHIRCQLGFYGGVPTDLHTTQNPTEGSYYDQDQYMDNTLTMFKSLREKYGNQFHILHDVHERLFPNQAIQFAKEVEQYKPYFIEDILPPNQTEWLDNIRSQSSVSLGLGELFNNPEEWKSLIANRRIDFIRCHVSQIGGITPALKLGHLCQNFGVRIAWHCPPDMTPIGAAVNTHLNVHLHNAAIQEHVEYNGNTHKVFPNAAEPINGYLYASEIAGIGVEIDREAAAEFP 378
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dfhC01 C:2-110,C:364-380 Enolase-like, N-terminal domain                                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3dfhC01           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee......eeeeeeee.....eeeee....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee..--------------------hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhh.....eee.....hhhhhhhhhhh....ee........hhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhh.........ee............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------MR_MLE_1  PDB: C:91-116   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dfh C   2 SLKETIISDIHCIITKPDRHNLITVVVETNEGVTGFGCATFQQRPLAVKTMVDEYLKPILIGKNANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKLAGMPLHQLFGGKSRDAIPVYTHATSDTMEGIYDLVEGFLEKGYKHIRCQLGF--------------------DQDQYMDNTLTMFKSLREKYGNQFHILHDVHERLFPNQAIQFAKEVEQYKPYFIEDILPPNQTEWLDNIRSQSSVSLGLGELFNNPEEWKSLIANRRIDFIRCHVSQIGGITPALKLGHLCQNFGVRIAWHCPPDMTPIGAAVNTHLNVHLHNAAIQEHVEYNGNTHKVFPNAAEPINGYLYASEIAGIGVEIDREAAAEFP 380
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      |  -         -       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371         
                                                                                                                                                                                      158                  179

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 3DFH)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: Enolase-like, N-terminal domain (130)

Vibrionales bacterium swat-3. Organism_taxid: 391574. Strain: swat-3. (1)

1a	3dfhA01	A:2-110,A:364-380
1b	3dfhB01	B:2-110,B:364-380
1c	3dfhC01	C:2-110,C:364-380

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (IMAND_VIBBS | A5KUH4)

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: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.

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	3dfh
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	IMAND_VIBBS \| A5KUH4	:	3r25 3sbf

(no "Related Entries Specified in the PDB File" available for 3DFH)

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