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Title :   CRYSTAL STRUCTURE OF YFAU, A METAL ION DEPENDENT CLASS II ALDOLASE FROM ESCHERICHIA COLI K12 - MG-PYRUVATE PRODUCT COMPLEX

Authors :   D. Rea, J. F. Rakus, J. A. Gerlt, V. Fulop, T. D. H. Bugg, D. I. Roper

Date :   26 Jun 08 (Deposition) - 09 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

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

Keywords :   Lyase, (Beta/Alpha)8 Barrel, 2-Keto-3-Deoxy Sugar Aldolase, Escherichia Coli K-12 Protein Yfau, Degradation Of Homoprotocatechuate, Pyruvate, Class Ii Aldolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Rea, R. Hovington, J. F. Rakus, J. A. Gerlt, V. Fulop, T. D. H. Bugg, D. I. Roper
Crystal Structure And Functional Assignment Of Yfau, A Metal Ion Dependent Class Ii Aldolase From Escherichia Coli K12.
Biochemistry V. 47 9955 2008
PubMed-ID: 18754683 | Reference-DOI: 10.1021/BI800943G

Molecule 1 - YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
	Atcc	:	27325
	Chains	:	A, B, C
	EC Number	:	4.1.2.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7-YFAU
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PT7-7
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	UNCHARACTERIZED PROTEIN YFAU

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MG	3	Ligand/Ion	MAGNESIUM ION
3	PO4	3	Ligand/Ion	PHOSPHATE ION
4	PYR	3	Ligand/Ion	PYRUVIC ACID

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PO4	6	Ligand/Ion	PHOSPHATE ION
4	PYR	6	Ligand/Ion	PYRUVIC ACID

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:151 , GLU A:153 , ASP A:179 , PYR A:302 , HOH A:2040 , HOH A:2154	BINDING SITE FOR RESIDUE MG A 301
02	AC2	SOFTWARE	ARG A:74 , GLN A:151 , GLU A:153 , PHE A:174 , GLY A:176 , PRO A:177 , ALA A:178 , ASP A:179 , LEU A:216 , MG A:301	BINDING SITE FOR RESIDUE PYR A 302
03	AC3	SOFTWARE	GLN B:151 , GLU B:153 , ASP B:179 , PYR B:302 , HOH B:2035 , HOH C:2094	BINDING SITE FOR RESIDUE MG B 301
04	AC4	SOFTWARE	ARG B:74 , GLN B:151 , GLU B:153 , PHE B:174 , GLY B:176 , PRO B:177 , ALA B:178 , ASP B:179 , MG B:301 , HOH C:2094	BINDING SITE FOR RESIDUE PYR B 302
05	AC5	SOFTWARE	HOH A:2112 , GLN C:151 , GLU C:153 , ASP C:179 , PYR C:302 , HOH C:2112	BINDING SITE FOR RESIDUE MG C 301
06	AC6	SOFTWARE	ARG C:74 , GLN C:151 , GLU C:153 , GLY C:176 , PRO C:177 , ALA C:178 , ASP C:179 , LEU C:216 , MG C:301	BINDING SITE FOR RESIDUE PYR C 302
07	AC7	SOFTWARE	THR A:27 , ALA A:29 , ASP A:56 , HIS A:59 , HOH A:2201 , HOH A:2202 , HOH A:2203	BINDING SITE FOR RESIDUE PO4 A1257
08	AC8	SOFTWARE	THR B:27 , ALA B:29 , ASP B:56 , HIS B:59 , HOH B:2178 , HOH B:2179	BINDING SITE FOR RESIDUE PO4 B1257
09	AC9	SOFTWARE	THR C:27 , THR C:28 , ALA C:29 , ASP C:56 , HIS C:59 , HOH C:2157 , HOH C:2158	BINDING SITE FOR RESIDUE PO4 C1257
10	BC1	SOFTWARE	GLY C:78 , PRO C:97 , MET C:98 , GLN C:104	BINDING SITE FOR RESIDUE GOL C1258

(no "SS Bond" information available for 2VWT)

Asymmetric Unit

No.	Residues
1	Pro B:115	-	Pro B:116
2	Pro C:115	-	Pro C:116

(no "SAP(SNP)/Variant" information available for 2VWT)

(no "PROSITE Motif" information available for 2VWT)

(no "Exon" information available for 2VWT)

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:256
 aligned with RHMA_ECOLI | P76469 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:256
                                    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      
           RHMA_ECOLI     1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
               SCOP domains d2vwta_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhhheeeeee.hhhhhhhhhhhhh.....eeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vwt A   1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
                                    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

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with RHMA_ECOLI | P76469 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:256
                                    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      
           RHMA_ECOLI     1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
               SCOP domains d2vwtb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh..eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhhheeeeee.hhhhhhhhhhhhh.....eeeehhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vwt B   1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
                                    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

Chain C from PDB  Type:PROTEIN  Length:256
 aligned with RHMA_ECOLI | P76469 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:256
                                    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      
           RHMA_ECOLI     1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
               SCOP domains d2vwtc_ C: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhhhhhhheeeee..hhhhhhhhhhhhhh....eeeehhhhhhhhh..........hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vwt C   1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
                                    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

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Phosphoenolpyruvate/pyruvate domain (92)

Family: automated matches (16)

Protein domain: automated matches (16)

Escherichia coli K-12 [TaxId: 83333] (2)

1a	d2vwta_	A:
1b	d2vwtb_	B:
1c	d2vwtc_	C:

(no "CATH Domain" information available for 2VWT)

(no "Pfam Domain" information available for 2VWT)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RHMA_ECOLI | P76469)

molecular function
	GO:0016832	aldehyde-lyase activity	Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
	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.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006725	cellular aromatic compound metabolic process	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
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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	Cis Peptide Bonds
		Pro B:115 - Pro B:116	[ RasMol ]
		Pro C:115 - Pro C:116	[ RasMol ]

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	2vwt
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	RHMA_ECOLI \| P76469	:	2vws

2vws	CRYSTAL STRUCTURE OF YFAU, A METAL ION DEPENDENT CLASS II ALDOLASE FROM ESCHERICHIA COLI K12

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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