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Title :   CLASS II ALDOLASE HPCH - MAGNESIUM - OXAMATE COMPLEX

Authors :   D. Rea, V. Fulop, T. D. H. Bugg, D. I. Roper

Date :   06 Jul 07 (Deposition) - 02 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Lyase, Class Ii Aldolase, Homoprotocatechuate, Aromatic Degradation, Aromatic Hydrocarbons Catabolismhomoprotocatechuate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Rea, V. Fulop, T. D. H. Bugg, D. I. Roper
Structure And Mechanism Of Hpch: A Metal Ion Dependent Class Ii Aldolase From The Homoprotocatechuate Degradation Pathway Of Escherichia Coli.
J. Mol. Biol. V. 373 866 2007
PubMed-ID: 17881002 | Reference-DOI: 10.1016/J.JMB.2007.06.048

Molecule 1 - 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
	Chains	:	A, B
	EC Number	:	4.1.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector	:	PPROEX-HTA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	498388
	Strain	:	C
	Synonym	:	HHED ALDOLASE, 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	OXM	2	Ligand/Ion	OXAMIC ACID
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	OXM	6	Ligand/Ion	OXAMIC ACID
3	PO4	6	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:147 , GLU A:149 , ASP A:175 , OXM A:302 , HOH A:2027 , HOH A:2085	BINDING SITE FOR RESIDUE MG A 301
2	AC2	SOFTWARE	ARG A:70 , GLN A:147 , GLU A:149 , GLY A:172 , PRO A:173 , ALA A:174 , ASP A:175 , LEU A:212 , MG A:301 , HOH A:2085	BINDING SITE FOR RESIDUE OXM A 302
3	AC3	SOFTWARE	GLU B:149 , ASP B:175 , OXM B:302 , HOH B:2031 , HOH B:2096	BINDING SITE FOR RESIDUE MG B 301
4	AC4	SOFTWARE	ARG B:70 , GLN B:147 , GLU B:149 , GLY B:172 , PRO B:173 , ALA B:174 , ASP B:175 , LEU B:212 , MG B:301 , HOH B:2096	BINDING SITE FOR RESIDUE OXM B 302
5	AC5	SOFTWARE	LYS A:6 , LYS A:10 , ARG A:109 , GLU A:164 , GLY A:165 , ASP A:167 , HOH A:2109	BINDING SITE FOR RESIDUE PO4 A1260
6	AC6	SOFTWARE	LYS B:6 , LYS B:10 , ARG B:109 , GLU B:164 , GLY B:165 , ASP B:167	BINDING SITE FOR RESIDUE PO4 B1260

(no "SS Bond" information available for 2V5K)

Asymmetric Unit

No.	Residues
1	Pro A:111	-	Pro A:112
2	Pro B:111	-	Pro B:112

(no "SAP(SNP)/Variant" information available for 2V5K)

(no "PROSITE Motif" information available for 2V5K)

(no "Exon" information available for 2V5K)

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:261
 aligned with HPCH_ECOLX | Q47098 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:261
                                     1                                                                                                                                                                                                                                                           
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 
           HPCH_ECOLX     - ---------MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFGA 252
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh....hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh..............hhhhh.....hhhhhhhhhheeeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v5k A  -8 TENLYFQGAMENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFGA 252
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with HPCH_ECOLX | Q47098 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:261
                                     1                                                                                                                                                                                                                                                           
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 
           HPCH_ECOLX     - ---------MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFGA 252
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------HpcH_HpaI-2v5kB01 B:15-242                                                                                                                                                                                                          ---------- Pfam domains (1)
           Pfam domains (2) -----------------------HpcH_HpaI-2v5kB02 B:15-242                                                                                                                                                                                                          ---------- Pfam domains (2)
         Sec.struct. author hhhhhhh....hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh..........hhhhhhhhh.....hhhhhhhhhheeeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v5k B  -8 TENLYFQGAMENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAPYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARAAEALAARFGA 252
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

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 2V5K)

(no "CATH Domain" information available for 2V5K)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PK_TIM (63)

Family: HpcH_HpaI (8)

Escherichia coli (2)

1a	HpcH_HpaI-2v5kB01	B:15-242
1b	HpcH_HpaI-2v5kB02	B:15-242

Asymmetric Unit(hide GO term definitions)

Chain A,B (HPCH_ECOLX | Q47098)

molecular function
	GO:0018802	2,4-dihydroxyhept-2-ene-1,7-dioate aldolase activity	Catalysis of the reaction: 2,4-dihydroxy-hept-trans-2-ene-1,7-dioate = pyruvate + succinic semialdehyde.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	GO:0010124	phenylacetate catabolic process	The chemical reactions and pathways resulting in the breakdown of phenylacetate.

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	Cis Peptide Bonds
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		Pro B:111 - Pro B:112	[ RasMol ]

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	HPCH_ECOLX \| Q47098	:	2v5j

2v5j	APO CLASS II ALDOLASE HPCH

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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