3BQB - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   HEXAGONAL KRISTAL FORM OF 2-KETO-3-DEOXYARABINONATE DEHYDRATASE

Authors :   T. M. Barends, S. Brouns, P. Worm, J. Akerboom, A. Turnbull, L. Salmon

Date :   20 Dec 07 (Deposition) - 08 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,X,Y,Z
Biol. Unit 1: A,X,Y,Z  (1x)
Biol. Unit 2: A,X  (1x)
Biol. Unit 3: Y,Z  (1x)

Keywords :   Fah-Family Fold, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. J. Brouns, T. R. M. Barends, P. Worm, J. Akerboom, A. P. Turnbull, L. Salmon, J. Van Der Oost
Structural Insight Into Substrate Binding And Catalysis Of Novel 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Illustrates Common Mechanistic Features Of The Fah Superfamily
J. Mol. Biol. V. 379 357 2008
PubMed-ID: 18448118 | Reference-DOI: 10.1016/J.JMB.2008.03.064

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
	Chains	:	A, X, Z, Y
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24
	Expression System Strain	:	HB101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 6-298
	Gene	:	DKAD
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	273057
	Strain	:	P2
	Synonym	:	2-KETO-3-DEOXYARABINONATE DEHYDRATASE

		1	2	3	4
Asymmetric Unit	:	A	X	Y	Z
Biological Unit 1 (1x)	:	A	X	Y	Z
Biological Unit 2 (1x)	:	A	X
Biological Unit 3 (1x)	:			Y	Z

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU Y:143 , GLU Y:145 , ASP Y:164 , LYS Y:182	BINDING SITE FOR RESIDUE MG Y 294
2	AC2	SOFTWARE	GLU Z:143 , GLU Z:145 , ASP Z:164 , LYS Z:182	BINDING SITE FOR RESIDUE MG Z 294
3	AC3	SOFTWARE	GLU X:143 , GLU X:145 , ASP X:164 , LYS X:182	BINDING SITE FOR RESIDUE MG X 294
4	AC4	SOFTWARE	GLU A:143 , GLU A:145 , ASP A:164 , LYS A:182	BINDING SITE FOR RESIDUE MG A 294

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

Asymmetric Unit

No.	Residues
1	Gly A:191	-	Pro A:192
2	Gly X:191	-	Pro X:192
3	Gly Z:191	-	Pro Z:192
4	Gly Y:191	-	Pro Y:192

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

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

(no "Exon" information available for 3BQB)

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:282
 aligned with KDAD_SULSO | Q97UA0 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:291
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 
           KDAD_SULSO     6 MKLFRVVKRGYYISYAILDNSTIIRLDEDPIKALMRYSENKEVLGDRVTGIDYQSLLKSFQINDIRITKPIDPPEVWGSGISYEMARERYSEENVAKILGKTIYEKVYDAVRPEIFFKATPNRCVGHGEAIAVRSDSEWTLPEPELAVVLDSNGKILGYTIMDDVSARDLEAENPLYLPQSKIYAGCCAFGPVIVTSDEIKNPYSLDITLKIVREGRVFFEGSVNTNKMRRKIEEQIQYLIRDNPIPDGTILTTGTAIVPGRDKGLKDEDIVEITISNIGTLITPVKKRRK 296
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee.....eeee..hhhhhhhhhhhhh...eeeee..hhhhhhhhhee..eee........eee......---------...ee..eehhhhhhhh.....eeeehhh.ee.....eee......ee..eeeeeee.....eeeeeeeee.eehhhhhhh..hhhhhhh....eeeeeeee.hhhh......eeeeeeee..eeeeeeeee.hhh..hhhhhhhhhh........eeee.................eeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bqb A   1 MKLFRVVKRGYYISYAILDNSTIIRLDEDPIKALMRYSENKEVLGDRVTGIDYQSLLKSFQINDIRITKPIDPPEVWGSGISYE---------NVAKILGKTIYEKVYDAVRPEIFFKATPNRCVGHGEAIAVRSDSEWTLPEPELAVVLDSNGKILGYTIMDDVSARDLEAENPLYLPQSKIYAGCCAFGPVIVTSDEIKNPYSLDITLKIVREGRVFFEGSVNTNKMRRKIEEQIQYLIRDNPIPDGTILTTGTAIVPGRDKGLKDEDIVEITISNIGTLITPVKKRRK 291
                                    10        20        30        40        50        60        70        80   |     -   |   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
                                                                                                              84        94

Chain X from PDB  Type:PROTEIN  Length:291
 aligned with KDAD_SULSO | Q97UA0 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:291
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 
           KDAD_SULSO     6 MKLFRVVKRGYYISYAILDNSTIIRLDEDPIKALMRYSENKEVLGDRVTGIDYQSLLKSFQINDIRITKPIDPPEVWGSGISYEMARERYSEENVAKILGKTIYEKVYDAVRPEIFFKATPNRCVGHGEAIAVRSDSEWTLPEPELAVVLDSNGKILGYTIMDDVSARDLEAENPLYLPQSKIYAGCCAFGPVIVTSDEIKNPYSLDITLKIVREGRVFFEGSVNTNKMRRKIEEQIQYLIRDNPIPDGTILTTGTAIVPGRDKGLKDEDIVEITISNIGTLITPVKKRRK 296
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee.....eeee..hhhhhhhhhhhhh...eeeee..hhhhhhhhhee..eee........eee..................ee..eehhhhhhhh.....eeeehhh.ee.....eee......ee..eeeeeee.....eeeeeeeee.eehhhhhhh..hhhhhhh....eeeeeeeee.hhh......eeeeeeee..eeeeeeeee.hhh..hhhhhhhhhhh.......eeeeeee..............eeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bqb X   1 MKLFRVVKRGYYISYAILDNSTIIRLDEDPIKALMRYSENKEVLGDRVTGIDYQSLLKSFQINDIRITKPIDPPEVWGSGISYEMARERYSEENVAKILGKTIYEKVYDAVRPEIFFKATPNRCVGHGEAIAVRSDSEWTLPEPELAVVLDSNGKILGYTIMDDVSARDLEAENPLYLPQSKIYAGCCAFGPVIVTSDEIKNPYSLDITLKIVREGRVFFEGSVNTNKMRRKIEEQIQYLIRDNPIPDGTILTTGTAIVPGRDKGLKDEDIVEITISNIGTLITPVKKRRK 291
                                    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

Chain Y from PDB  Type:PROTEIN  Length:282
 aligned with KDAD_SULSO | Q97UA0 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:291
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 
           KDAD_SULSO     6 MKLFRVVKRGYYISYAILDNSTIIRLDEDPIKALMRYSENKEVLGDRVTGIDYQSLLKSFQINDIRITKPIDPPEVWGSGISYEMARERYSEENVAKILGKTIYEKVYDAVRPEIFFKATPNRCVGHGEAIAVRSDSEWTLPEPELAVVLDSNGKILGYTIMDDVSARDLEAENPLYLPQSKIYAGCCAFGPVIVTSDEIKNPYSLDITLKIVREGRVFFEGSVNTNKMRRKIEEQIQYLIRDNPIPDGTILTTGTAIVPGRDKGLKDEDIVEITISNIGTLITPVKKRRK 296
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee.....eeee..hhhhhhhhhhhhh...eeee...hhhhhhhhhee..eeee.......eeeee....---------...ee..eehhhhhhhh...eeeeeehhh.ee.....eee......ee..eeeeeee.....eeeeeeeee.eehhhhhhh..hhhhhhh....eeeeeeeee.hhh......eeeeeee....eeeeeeee.hhh..hhhhhhhhhhh........eeeeee..............eeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bqb Y   1 MKLFRVVKRGYYISYAILDNSTIIRLDEDPIKALMRYSENKEVLGDRVTGIDYQSLLKSFQINDIRITKPIDPPEVWGSGISYE---------NVAKILGKTIYEKVYDAVRPEIFFKATPNRCVGHGEAIAVRSDSEWTLPEPELAVVLDSNGKILGYTIMDDVSARDLEAENPLYLPQSKIYAGCCAFGPVIVTSDEIKNPYSLDITLKIVREGRVFFEGSVNTNKMRRKIEEQIQYLIRDNPIPDGTILTTGTAIVPGRDKGLKDEDIVEITISNIGTLITPVKKRRK 291
                                    10        20        30        40        50        60        70        80   |     -   |   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
                                                                                                              84        94

Chain Z from PDB  Type:PROTEIN  Length:282
 aligned with KDAD_SULSO | Q97UA0 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:291
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 
           KDAD_SULSO     6 MKLFRVVKRGYYISYAILDNSTIIRLDEDPIKALMRYSENKEVLGDRVTGIDYQSLLKSFQINDIRITKPIDPPEVWGSGISYEMARERYSEENVAKILGKTIYEKVYDAVRPEIFFKATPNRCVGHGEAIAVRSDSEWTLPEPELAVVLDSNGKILGYTIMDDVSARDLEAENPLYLPQSKIYAGCCAFGPVIVTSDEIKNPYSLDITLKIVREGRVFFEGSVNTNKMRRKIEEQIQYLIRDNPIPDGTILTTGTAIVPGRDKGLKDEDIVEITISNIGTLITPVKKRRK 296
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee.....eeee..hhhhhhhhhhhhh...eeee...hhhhhhhhhee..eeee.......eeeee....---------...ee..eehhhhhhhh...eeeeeehhh.ee.....eee......eeeeeeeeeee.....eeeeeeeeeeeehhhhhhh..hhhhhhh....eeeeeeee.hhhh.hhhh.eeeeeeee..eeeeeeeee.hhh..hhhhhhhhhhh........eee.................eeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bqb Z   1 MKLFRVVKRGYYISYAILDNSTIIRLDEDPIKALMRYSENKEVLGDRVTGIDYQSLLKSFQINDIRITKPIDPPEVWGSGISYE---------NVAKILGKTIYEKVYDAVRPEIFFKATPNRCVGHGEAIAVRSDSEWTLPEPELAVVLDSNGKILGYTIMDDVSARDLEAENPLYLPQSKIYAGCCAFGPVIVTSDEIKNPYSLDITLKIVREGRVFFEGSVNTNKMRRKIEEQIQYLIRDNPIPDGTILTTGTAIVPGRDKGLKDEDIVEITISNIGTLITPVKKRRK 291
                                    10        20        30        40        50        60        70        80   |     -   |   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
                                                                                                              84        94

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 3BQB)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,X,Y,Z (KDAD_SULSO | Q97UA0)

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:0016836	hydro-lyase activity	Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
	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.
biological process
	GO:0019571	D-arabinose catabolic process	The chemical reactions and pathways resulting in the breakdown of D-arabinose, the D-enantiomer of arabino-pentose.
	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: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.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:191 - Pro A:192	[ RasMol ]
		Gly X:191 - Pro X:192	[ RasMol ]
		Gly Y:191 - Pro Y:192	[ RasMol ]
		Gly Z:191 - Pro Z:192	[ RasMol ]

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	3bqb
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	KDAD_SULSO \| Q97UA0	:	2q18 2q19 2q1a 2q1c 2q1d

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

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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