4E38 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PROBABLE KETO-HYDROXYGLUTARATE-ALDOLASE FROM VIBRIONALES BACTERIUM SWAT-3 (TARGET EFI-502156)

Authors :   Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washin A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H J. A. Gerlt, K. N. Allen, D. Dunaway-Mariano, S. C. Almo, Enzyme Funct Initiative (Efi)

Date :   09 Mar 12 (Deposition) - 21 Mar 12 (Release) - 21 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.64

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

Keywords :   Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H. J. Imker, K. N. Allen, D. Dunaway-Mariano, J. A. Gerlt, S. C. Almo
Crystal Structure Of Probable Keto-Hydroxyglutarate-Aldolas From Vibrionales Bacterium Swat-3 (Target Efi-502156)
To Be Published
PubMed: search

Molecule 1 - KETO-HYDROXYGLUTARATE-ALDOLASE/KETO-DEOXY-PHOSPHOGLUCONATE ALDOLASE
	Chains	:	A, B, C
	EC Number	:	4.1.3.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	VSWAT3_13722
	Organism Scientific	:	VIBRIONALES BACTERIUM SWAT-3
	Organism Taxid	:	391574

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 7)

No.	Name	Count	Type	Full Name
1	CL	7	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:69 , SER A:89 , PRO A:90 , LYS A:129 , HOH A:437 , HOH A:522	BINDING SITE FOR RESIDUE CL A 301
2	AC2	SOFTWARE	ASN A:113 , ASN B:113 , ASN C:113	BINDING SITE FOR RESIDUE CL A 302
3	AC3	SOFTWARE	PRO A:132 , GLU A:134 , ALA A:135 , GLY A:158 , SER C:144 , HOH C:470 , HOH C:618	BINDING SITE FOR RESIDUE CL A 303
4	AC4	SOFTWARE	THR B:69 , VAL B:88 , SER B:89 , PRO B:90 , LYS B:129 , HOH B:540	BINDING SITE FOR RESIDUE CL B 301
5	AC5	SOFTWARE	HOH A:420 , HOH A:440 , PRO B:132 , GLU B:134 , ALA B:135 , GLY B:158	BINDING SITE FOR RESIDUE CL B 302
6	AC6	SOFTWARE	THR C:69 , SER C:89 , PRO C:90 , LYS C:129	BINDING SITE FOR RESIDUE CL C 301
7	AC7	SOFTWARE	HOH B:426 , HOH B:541 , PRO C:132 , GLU C:134 , ALA C:135 , GLY C:158	BINDING SITE FOR RESIDUE CL C 302

(no "SS Bond" information available for 4E38)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:131	-	Pro A:132
2	Phe B:131	-	Pro B:132
3	Phe C:131	-	Pro C:132

(no "SAP(SNP)/Variant" information available for 4E38)

(no "PROSITE Motif" information available for 4E38)

(no "Exon" information available for 4E38)

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:213
 aligned with A5KUH7_VIBBS | A5KUH7 from UniProtKB/TrEMBL  Length:209

    Alignment length:213
                                1                                                                                                                                                                                                                
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
         A5KUH7_VIBBS     - ----MSTINNQLKALKVIPVIAIDNAEDIIPLGKVLAENGLPAAEITFRSDAAVEAIRLLRQAQPEMLIGAGTILNGEQALAAKEAGATFVVSPGFNPNTVRACQEIGIDIVPGVNNPSTVEAALEMGLTTLKFFPAEASGGISMVKSLVGPYGDIRLMPTGGITPSNIDNYLAIPQVLACGGTWMVDKKLVTNGEWDEIARLTREIVEQVNP 209
               SCOP domains d4e38a_ A: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh..eee....hhhhhhhhhhhh.eee.ee.hhhhhhhhhhh...eeee......hhhhhhhhhhh.....eeee.......hhhhhhh......eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e38 A  -3 FQSMMSTINNQLKALKVIPVIAIDNAEDIIPLGKVLAENGLPAAEITFRSDAAVEAIRLLRQAQPEMLIGAGTILNGEQALAAKEAGATFVVSPGFNPNTVRACQEIGIDIVPGVNNPSTVEAALEMGLTTLKFFPAEASGGISMVKSLVGPYGDIRLMPTGGITPSNIDNYLAIPQVLACGGTWMVDKKLVTNGEWDEIARLTREIVEQVNP 209
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with A5KUH7_VIBBS | A5KUH7 from UniProtKB/TrEMBL  Length:209

    Alignment length:213
                                1                                                                                                                                                                                                                
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
         A5KUH7_VIBBS     - ----MSTINNQLKALKVIPVIAIDNAEDIIPLGKVLAENGLPAAEITFRSDAAVEAIRLLRQAQPEMLIGAGTILNGEQALAAKEAGATFVVSPGFNPNTVRACQEIGIDIVPGVNNPSTVEAALEMGLTTLKFFPAEASGGISMVKSLVGPYGDIRLMPTGGITPSNIDNYLAIPQVLACGGTWMVDKKLVTNGEWDEIARLTREIVEQVNP 209
               SCOP domains d4e38b_ B: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhh.eeeeee.hhhhhhhhhhh...eeee......hhhhhhhhhhh.....eeee.......hhhhhhh......eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e38 B  -3 FQSMMSTINNQLKALKVIPVIAIDNAEDIIPLGKVLAENGLPAAEITFRSDAAVEAIRLLRQAQPEMLIGAGTILNGEQALAAKEAGATFVVSPGFNPNTVRACQEIGIDIVPGVNNPSTVEAALEMGLTTLKFFPAEASGGISMVKSLVGPYGDIRLMPTGGITPSNIDNYLAIPQVLACGGTWMVDKKLVTNGEWDEIARLTREIVEQVNP 209
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206

Chain C from PDB  Type:PROTEIN  Length:227
 aligned with A5KUH7_VIBBS | A5KUH7 from UniProtKB/TrEMBL  Length:209

    Alignment length:227
                                              1                                                                                                                                                                                                                
                                     -        |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
         A5KUH7_VIBBS     - ------------------MSTINNQLKALKVIPVIAIDNAEDIIPLGKVLAENGLPAAEITFRSDAAVEAIRLLRQAQPEMLIGAGTILNGEQALAAKEAGATFVVSPGFNPNTVRACQEIGIDIVPGVNNPSTVEAALEMGLTTLKFFPAEASGGISMVKSLVGPYGDIRLMPTGGITPSNIDNYLAIPQVLACGGTWMVDKKLVTNGEWDEIARLTREIVEQVNP 209
               SCOP domains d4e38c_ C: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhh.eeeeee.hhhhhhhhhhh...eeee......hhhhhhhhhhh.....eeee.......hhhhhhh......eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e38 C -17 HHSSGVDLGTENLYFQSMMSTINNQLKALKVIPVIAIDNAEDIIPLGKVLAENGLPAAEITFRSDAAVEAIRLLRQAQPEMLIGAGTILNGEQALAAKEAGATFVVSPGFNPNTVRACQEIGIDIVPGVNNPSTVEAALEMGLTTLKFFPAEASGGISMVKSLVGPYGDIRLMPTGGITPSNIDNYLAIPQVLACGGTWMVDKKLVTNGEWDEIARLTREIVEQVNP 209
                                    -8         2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: automated matches (113)

Protein domain: automated matches (113)

Vibrionales bacterium [TaxId: 391574] (1)

1a	d4e38a_	A:
1b	d4e38b_	B:
1c	d4e38c_	C:

(no "CATH Domain" information available for 4E38)

(no "Pfam Domain" information available for 4E38)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (A5KUH7_VIBBS | A5KUH7)

molecular function
	GO:0008700	4-hydroxy-2-oxoglutarate aldolase activity	Catalysis of the reaction: 4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate.
	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.
biological process
	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/Biological Unit
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	Cis Peptide Bonds
		Phe A:131 - Pro A:132	[ RasMol ]
		Phe B:131 - Pro B:132	[ RasMol ]
		Phe C:131 - Pro C:132	[ RasMol ]

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	4e38
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(no "Related Entries Specified in the PDB File" available for 4E38)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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