3HPF - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE MUTANT Y90F OF DIVERGENT GALACTARATE DEHYDRATASE FROM OCEANOBACILLUS IHEYENSIS COMPLEXED WITH MG AND GALACTARATE

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

Date :   04 Jun 09 (Deposition) - 22 Dec 09 (Release) - 22 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Galactarate Dehydratase, Galactarate, X-Ray Structure, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. F. Rakus, C. Kalyanaraman, A. A. Fedorov, E. V. Fedorov, F. P. Mills-Groninger, R. Toro, J. Bonanno, K. Bain, J. M. Sauder, S. K. Burley, S. C. Almo, M. P. Jacobson, J. A. Gerlt
Computation-Facilitated Assignment Of The Function In The Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase From Oceanobacillus Iheyensis .
Biochemistry V. 48 11546 2009
PubMed-ID: 19883118 | Reference-DOI: 10.1021/BI901731C
(for further references see the PDB file header)

Molecule 1 - MUCONATE CYCLOISOMERASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	OB2843
	Mutation	:	YES
	Organism Scientific	:	OCEANOBACILLUS IHEYENSIS HTE831
	Organism Taxid	:	221109
	Strain	:	DSM 14371, JCM 11309, KCTC 3954, HTE831

		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 (2, 6)

No.	Name	Count	Type	Full Name
1	GAE	2	Ligand/Ion	D-GALACTARIC ACID
2	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	GAE	2	Ligand/Ion	D-GALACTARIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 8)

No.	Name	Count	Type	Full Name
1	GAE	8	Ligand/Ion	D-GALACTARIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:15 , ASP A:42 , HIS A:45 , TYR A:89 , ARG A:162 , TYR A:164 , ASP A:193 , GLU A:221 , HIS A:246 , PHE A:271 , THR A:296 , THR A:297 , GLN A:298 , ARG A:385 , HOH A:397 , HOH A:398 , MG A:401 , MG A:402 , HOH A:518 , HOH A:536 , HOH A:597	BINDING SITE FOR RESIDUE GAE A 411
2	AC2	SOFTWARE	ASP A:193 , GLU A:221 , HIS A:246 , HOH A:397 , GAE A:411	BINDING SITE FOR RESIDUE MG A 401
3	AC3	SOFTWARE	ASP A:42 , HIS A:45 , THR A:297 , GAE A:411	BINDING SITE FOR RESIDUE MG A 402
4	AC4	SOFTWARE	ARG B:15 , ASP B:42 , HIS B:45 , TYR B:89 , ARG B:162 , TYR B:164 , ASP B:193 , GLU B:221 , HIS B:246 , PHE B:271 , THR B:296 , THR B:297 , GLN B:298 , ARG B:385 , MG B:401 , MG B:402 , HOH B:404 , HOH B:451 , HOH B:537 , HOH B:595 , HOH B:611	BINDING SITE FOR RESIDUE GAE B 411
5	AC5	SOFTWARE	ASP B:193 , GLU B:221 , HIS B:246 , HOH B:404 , GAE B:411	BINDING SITE FOR RESIDUE MG B 401
6	AC6	SOFTWARE	ASP B:42 , HIS B:45 , THR B:297 , GAE B:411	BINDING SITE FOR RESIDUE MG B 402

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

Asymmetric Unit

No.	Residues
1	Leu A:46	-	Pro A:47
2	Leu B:46	-	Pro B:47

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

(no "PROSITE Motif" information available for 3HPF)

(no "Exon" information available for 3HPF)

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:387
 aligned with GALRD_OCEIH | Q8EMJ9 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:387
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       
          GALRD_OCEIH     1 MKITDLELHAVGIPRHTGFVNKHVIVKIHTDEGLTGIGEMSDFSHLPLYSVDLHDLKQGLLSILLGQNPFDLMKINKELTDNFPETMYYYEKGSFIRNGIDNALHDLCAKYLDISVSDFLGGRVKEKIKVCYPIFRHRFSEEVESNLDVVRQKLEQGFDVFRLYVGKNLDADEEFLSRVKEEFGSRVRIKSYDFSHLLNWKDAHRAIKRLTKYDLGLEMIESPAPRNDFDGLYQLRLKTDYPISEHVWSFKQQQEMIKKDAIDIFNISPVFIGGLTSAKKAAYAAEVASKDVVLGTTQELSVGTAAMAHLGCSLTNINHTSDPTGPELYVGDVVKNRVTYKDGYLYAPDRSVKGLGIELDESLLAKYQVPDLSWDNVTVHQLQDRTA 387
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeeeeeeeee....eeeeee...........hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee..eee....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhh.......eee......hhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...........hhhhhh..........ee..eee.............hhhhhhhh..........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hpf A   1 MKITDLELHAVGIPRHTGFVNKHVIVKIHTDEGLTGIGEMSDFSHLPLYSVDLHDLKQGLLSILLGQNPFDLMKINKELTDNFPETMYYFEKGSFIRNGIDNALHDLCAKYLDISVSDFLGGRVKEKIKVCYPIFRHRFSEEVESNLDVVRQKLEQGFDVFRLYVGKNLDADEEFLSRVKEEFGSRVRIKSYDFSHLLNWKDAHRAIKRLTKYDLGLEMIESPAPRNDFDGLYQLRLKTDYPISEHVWSFKQQQEMIKKDAIDIFNISPVFIGGLTSAKKAAYAAEVASKDVVLGTTQELSVGTAAMAHLGCSLTNINHTSDPTGPELYVGDVVKNRVTYKDGYLYAPDRSVKGLGIELDESLLAKYQVPDLSWDNVTVHQLQDRTA 387
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380

Chain B from PDB  Type:PROTEIN  Length:387
 aligned with GALRD_OCEIH | Q8EMJ9 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:387
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       
          GALRD_OCEIH     1 MKITDLELHAVGIPRHTGFVNKHVIVKIHTDEGLTGIGEMSDFSHLPLYSVDLHDLKQGLLSILLGQNPFDLMKINKELTDNFPETMYYYEKGSFIRNGIDNALHDLCAKYLDISVSDFLGGRVKEKIKVCYPIFRHRFSEEVESNLDVVRQKLEQGFDVFRLYVGKNLDADEEFLSRVKEEFGSRVRIKSYDFSHLLNWKDAHRAIKRLTKYDLGLEMIESPAPRNDFDGLYQLRLKTDYPISEHVWSFKQQQEMIKKDAIDIFNISPVFIGGLTSAKKAAYAAEVASKDVVLGTTQELSVGTAAMAHLGCSLTNINHTSDPTGPELYVGDVVKNRVTYKDGYLYAPDRSVKGLGIELDESLLAKYQVPDLSWDNVTVHQLQDRTA 387
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeeeeeeeee.....eeeee...........hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee..eee....hhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhh.......eee......hhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...........hhhhhh..........ee..eee.............hhhhhhhh..........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hpf B   1 MKITDLELHAVGIPRHTGFVNKHVIVKIHTDEGLTGIGEMSDFSHLPLYSVDLHDLKQGLLSILLGQNPFDLMKINKELTDNFPETMYYFEKGSFIRNGIDNALHDLCAKYLDISVSDFLGGRVKEKIKVCYPIFRHRFSEEVESNLDVVRQKLEQGFDVFRLYVGKNLDADEEFLSRVKEEFGSRVRIKSYDFSHLLNWKDAHRAIKRLTKYDLGLEMIESPAPRNDFDGLYQLRLKTDYPISEHVWSFKQQQEMIKKDAIDIFNISPVFIGGLTSAKKAAYAAEVASKDVVLGTTQELSVGTAAMAHLGCSLTNINHTSDPTGPELYVGDVVKNRVTYKDGYLYAPDRSVKGLGIELDESLLAKYQVPDLSWDNVTVHQLQDRTA 387
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380

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 3HPF)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (GALRD_OCEIH | Q8EMJ9)

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: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: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
		Leu A:46 - Pro A:47	[ RasMol ]
		Leu B:46 - Pro B:47	[ RasMol ]

Biological Units
	Complete Structure
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	3hpf
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	GALRD_OCEIH \| Q8EMJ9	:	2oqy 3es7 3es8 3fyy 3gd6

3es7	THE SAME PROTEIN COMPLEXED WITH MALATE
3fyy	THE SAME PROTEIN WITHOUT LIGAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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