3PZR - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTALS STRUCTURE OF ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE FROM VIBRIO CHOLERAE WITH NADP AND PRODUCT OF S-CARBAMOYL-L-CYSTEINE

Authors :   A. G. Pavlovsky, N. Potente, R. E. Viola

Date :   14 Dec 10 (Deposition) - 04 Jan 12 (Release) - 04 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Nadp, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. G. Pavlovsky, X. Liu, C. R. Faehnle, N. Potente, R. E. Viola
Structural Characterization Of Inhibitors With Selectivity Against Members Of A Homologous Enzyme Family.
Chem. Biol. Drug Des. V. 79 128 2012
PubMed-ID: 22039970 | Reference-DOI: 10.1111/J.1747-0285.2011.01267.X

Molecule 1 - ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.2.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	VC_2036
	Organism Scientific	:	VIBRIO CHOLERAE
	Organism Taxid	:	666

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CYS	2	Mod. Amino Acid	CYSTEINE
2	NA	2	Ligand/Ion	SODIUM ION
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CYS	2	Mod. Amino Acid	CYSTEINE
2	NA	-1	Ligand/Ion	SODIUM ION
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CYS	2	Mod. Amino Acid	CYSTEINE
2	NA	-1	Ligand/Ion	SODIUM ION
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:133 , CYS A:134 , GLN A:161 , GLY A:165 , ILE A:229 , GLU A:240 , ARG A:267 , HIS A:274 , GLN A:350 , HOH A:623	BINDING SITE FOR RESIDUE CYS A 371
2	AC2	SOFTWARE	CYS B:134 , GLN B:161 , GLY B:165 , GLU B:240 , ARG B:267 , HIS B:274 , GLN B:350 , NAP B:372 , HOH B:639	BINDING SITE FOR RESIDUE CYS B 371
3	AC3	SOFTWARE	GLY A:7 , ARG A:9 , GLY A:10 , MET A:11 , VAL A:12 , SER A:35 , THR A:36 , SER A:37 , CYS A:71 , GLN A:72 , HOH A:387 , HOH A:394 , HOH A:410 , HOH A:423 , HOH A:446 , HOH A:500 , HOH A:551 , HOH A:610	BINDING SITE FOR RESIDUE NAP A 372
4	AC4	SOFTWARE	GLY A:210 , PHE A:212 , THR A:214 , HOH A:437 , HOH A:441 , HOH B:375	BINDING SITE FOR RESIDUE NA A 373
5	AC5	SOFTWARE	GLY B:7 , ARG B:9 , GLY B:10 , MET B:11 , VAL B:12 , THR B:36 , SER B:37 , CYS B:71 , GLN B:72 , GLY B:73 , ALA B:97 , GLY B:165 , GLN B:350 , CYS B:371 , HOH B:378 , HOH B:381 , HOH B:539 , HOH B:550 , HOH B:552 , HOH B:603 , HOH B:639 , HOH B:646 , HOH B:654 , HOH B:713	BINDING SITE FOR RESIDUE NAP B 372
6	AC6	SOFTWARE	GLY B:210 , PHE B:212 , HOH B:438 , HOH B:445 , HOH B:454 , HOH B:458	BINDING SITE FOR RESIDUE NA B 373

Asymmetric Unit

No.	Residues
1	A:134	-	A:371
2	B:134	-	B:371

(no "Cis Peptide Bond" information available for 3PZR)

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASD	PS01103	Aspartate-semialdehyde dehydrogenase signature.	DHAS1_VIBCH	261-275	2	A:261-275 B:261-275

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASD	PS01103	Aspartate-semialdehyde dehydrogenase signature.	DHAS1_VIBCH	261-275	2	A:261-275 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASD	PS01103	Aspartate-semialdehyde dehydrogenase signature.	DHAS1_VIBCH	261-275	2	- B:261-275

(no "Exon" information available for 3PZR)

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:371
 aligned with DHAS1_VIBCH | Q9KQG2 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:371
                                                                                                                                                                                                                                                                                                                                                                                                           370 
                                    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 
          DHAS1_VIBCH     1 MRVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGWKGYWIDAASTLRMDKEAIITLDPVNLKQILHGIHHGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSSELANPASSILDIDKKVAETMRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILGLQDSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDWVKVIPNERDITARELTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILAEK-   -
               SCOP domains d3pzra1 A:1-132,A:355-370 Aspartate beta-semialdehyde dehydrogenase                                                                 d3pzra2 A:133-354 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                                                   d3pzra1         - SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhhhhhheeeeee..................ee..hhhhhh...eeee..hhhhhhhhhhhhhhh....eeee..........eeeehhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...............ee...........hhhhhhhhhhhhhhh........ee....ee....eeeeeeeeee....hhhhhhhhhhh....eee...hhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeeeeee.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASD            ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pzr A   1 MRVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGWKGYWIDAASTLRMDKEAIITLDPVNLKQILHGIHHGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSSELANPASSILDIDKKVAETMRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILGLQDSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDWVKVIPNERDITARELTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILAEKC 371
                                    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

Chain B from PDB  Type:PROTEIN  Length:371
 aligned with DHAS1_VIBCH | Q9KQG2 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:371
                                                                                                                                                                                                                                                                                                                                                                                                           370 
                                    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 
          DHAS1_VIBCH     1 MRVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGWKGYWIDAASTLRMDKEAIITLDPVNLKQILHGIHHGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSSELANPASSILDIDKKVAETMRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILGLQDSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDWVKVIPNERDITARELTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILAEK-   -
               SCOP domains d3pzrb1 B:1-132,B:355-370 Aspartate beta-semialdehyde dehydrogenase                                                                 d3pzrb2 B:133-354 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                                                   d3pzrb1         - SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhhhhhheeeeee..................ee..hhhhhh...eeee..hhhhhhhhhhhhhhh....eeee..........eeeehhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh............................hhhhhhhhhhhhhhh........ee..........eeeeeeeeee....hhhhhhhhhhh....eee...hhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeeeeee.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASD            ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pzr B   1 MRVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGWKGYWIDAASTLRMDKEAIITLDPVNLKQILHGIHHGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSSELANPASSILDIDKKVAETMRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILGLQDSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDWVKVIPNERDITARELTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILAEKC 371
                                    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

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 "CATH Domain" information available for 3PZR)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (DHAS1_VIBCH | Q9KQG2)

molecular function
	GO:0003942	N-acetyl-gamma-glutamyl-phosphate reductase activity	Catalysis of the reaction: N-acetyl-L-glutamate 5-semialdehyde + NADP+ + phosphate = N-acetyl-5-glutamyl phosphate + NADPH + H+.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0004073	aspartate-semialdehyde dehydrogenase activity	Catalysis of the reaction: L-aspartate 4-semialdehyde + NADP(+) + phosphate = 4-phospho-L-aspartate + H(+) + NADPH.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
	GO:0071266	'de novo' L-methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of L-methionine, the L-enantiomer of (2S)-2-amino-4-(methylsulfanyl)butanoic acid, from simpler components.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0019877	diaminopimelate biosynthetic process	The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
	GO:0009097	isoleucine biosynthetic process	The chemical reactions and pathways resulting in the formation of isoleucine, (2R,3R)-2-amino-3-methylpentanoic acid.
	GO:0009085	lysine biosynthetic process	The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
	GO:0009089	lysine biosynthetic process via diaminopimelate	The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
	GO:0009086	methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0009088	threonine biosynthetic process	The chemical reactions and pathways resulting in the formation of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pzr)

Biological Units
	Complete Structure
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		Biological Unit 2	[ Jena3D ]

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	3pzr
		Family and Domain Information	:	ProDom \| SYSTERS
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	DHAS1_VIBCH \| Q9KQG2
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	1.2.1.11
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	DHAS1_VIBCH \| Q9KQG2
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	DHAS1_VIBCH \| Q9KQG2	:	1mb4 1mc4 3q0e 4r5m

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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