1Q7G - JenaLib

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Title :   HOMOSERINE DEHYDROGENASE IN COMPLEX WITH SUICIDE INHIBITOR COMPLEX NAD-5-HYDROXY-4-OXONORVALINE

Authors :   S. L. Jacques, I. A. Mirza, L. Ejim, K. Koteva, D. W. Hughes, K. Green, R. Kinach, J. F. Honek, H. K. Lai, A. M. Berghuis, G. D. Wright

Date :   18 Aug 03 (Deposition) - 21 Oct 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. L. Jacques, I. A. Mirza, L. Ejim, K. Koteva, D. W. Hughes, K. Green, R. Kinach, J. F. Honek, H. K. Lai, A. M. Berghuis, G. D. Wright
Enzyme Assisted Suicide: Molecular Basis For The Antifungal Activity Of 5-Hydroxy-4-Oxonorvaline By Potent Inhibition Of Homoserine Dehydrogenase
Chem. Biol. V. 10 989 2003
PubMed-ID: 14583265 | Reference-DOI: 10.1016/J.CHEMBIOL.2003.09.015
(for further references see the PDB file header)

Molecule 1 - HOMOSERINE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HOM6, YJR139C OR J2132
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	HDH

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION
2	NHO	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE-5-HYDROXY-4-OXONORVALINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:143 , VAL A:146 , GLY A:147 , ALA A:148 , LEU A:150	BINDING SITE FOR RESIDUE NA A 500
2	AC2	SOFTWARE	GLU B:143 , VAL B:146 , GLY B:147 , ALA B:148 , LEU B:150	BINDING SITE FOR RESIDUE NA B 501
3	AC3	SOFTWARE	ILE A:11 , GLY A:14 , VAL A:15 , VAL A:16 , GLU A:40 , ALA A:41 , ASN A:92 , THR A:93 , SER A:94 , ILE A:98 , PRO A:115 , LYS A:117 , ALA A:144 , SER A:174 , GLY A:175 , LYS A:223 , GLY A:338 , ALA A:339 , GLY A:340 , THR A:344 , HOH A:501 , HOH A:502	BINDING SITE FOR RESIDUE NHO A 361

(no "SS Bond" information available for 1Q7G)

(no "Cis Peptide Bond" information available for 1Q7G)

(no "SAP(SNP)/Variant" information available for 1Q7G)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HOMOSER_DHGENASE	PS01042	Homoserine dehydrogenase signature.	DHOM_YEAST	201-223	2	A:201-223 B:201-223

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YJR139C	1	YJR139C.1	X:690514-689435	1080	DHOM_YEAST	1-359	359	2	A:2-359 B:2-359	358 358

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:358
 aligned with DHOM_YEAST | P31116 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:358
                                    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       261       271       281       291       301       311       321       331       341       351        
           DHOM_YEAST     2 STKVVNVAVIGAGVVGSAFLDQLLAMKSTITYNLVLLAEAERSLISKDFSPLNVGSDWKAALAASTTKTLPLDDLIAHLKTSPKPVILVDNTSSAYIAGFYTKFVENGISIATPNKKAFSSDLATWKALFSNKPTNGFVYHEATVGAGLPIISFLREIIQTGDEVEKIEGIFSGTLSYIFNEFSTSQANDVKFSDVVKVAKKLGYTEPDPRDDLNGLDVARKVTIVGRISGVEVESPTSFPVQSLIPKPLESVKSADEFLEKLSDYDKDLTQLKKEAATENKVLRFIGKVDVATKSVSVGIEKYDYSHPFASLKGSDNVISIKTKRYTNPVVIQGAGAGAAVTAAGVLGDVIKIAQRL 359
               SCOP domains d1q7ga1 A:2-150,A:341-359 Homoserine dehydrogenase                                                                                                   d1q7ga2 A:151-340 Homoserine dehydrogenase                                                                                                                                                    d1q7ga1             SCOP domains
               CATH domains 1q7gA01 A:2-161,A:337-359 NAD(P)-binding Rossmann-like Domain                                                                                                   1q7gA02 A:162-336 Dihydrodipicolinate Reductase; domain 2                                                                                                                      1q7gA01                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhh.....eeeeeeee....eee...........hhhhhhhh......hhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhh.......eehhhhh.....hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhh.hhhhhhhhhhhhhhh.eeeeeeeeee....ee..eeeeee..hhhhhh....eeeeeee......eeeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HOMOSER_DHGENASE       ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-359 UniProt: 1-359 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                     Transcript 1
                 1q7g A   2 STKVVNVAVIGAGVVGSAFLDQLLAMKSTITYNLVLLAEAERSLISKDFSPLNVGSDWKAALAASTTKTLPLDDLIAHLKTSPKPVILVDNTSSAYIAGFYTKFVENGISIATPNKKAFSSDLATWKALFSNKPTNGFVYHEATVGAGLPIISFLREIIQTGDEVEKIEGIFSGTLSYIFNEFSTSQANDVKFSDVVKVAKKLGYTEPDPRDDLNGLDVARKVTIVGRISGVEVESPTSFPVQSLIPKPLESVKSADEFLEKLSDYDKDLTQLKKEAATENKVLRFIGKVDVATKSVSVGIEKYDYSHPFASLKGSDNVISIKTKRYTNPVVIQGAGAGAAVTAAGVLGDVIKIAQRL 359
                                    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       261       271       281       291       301       311       321       331       341       351

Chain B from PDB  Type:PROTEIN  Length:358
 aligned with DHOM_YEAST | P31116 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:358
                                    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       261       271       281       291       301       311       321       331       341       351        
           DHOM_YEAST     2 STKVVNVAVIGAGVVGSAFLDQLLAMKSTITYNLVLLAEAERSLISKDFSPLNVGSDWKAALAASTTKTLPLDDLIAHLKTSPKPVILVDNTSSAYIAGFYTKFVENGISIATPNKKAFSSDLATWKALFSNKPTNGFVYHEATVGAGLPIISFLREIIQTGDEVEKIEGIFSGTLSYIFNEFSTSQANDVKFSDVVKVAKKLGYTEPDPRDDLNGLDVARKVTIVGRISGVEVESPTSFPVQSLIPKPLESVKSADEFLEKLSDYDKDLTQLKKEAATENKVLRFIGKVDVATKSVSVGIEKYDYSHPFASLKGSDNVISIKTKRYTNPVVIQGAGAGAAVTAAGVLGDVIKIAQRL 359
               SCOP domains d1q7gb1 B:2-150,B:341-359 Homoserine dehydrogenase                                                                                                   d1q7gb2 B:151-340 Homoserine dehydrogenase                                                                                                                                                    d1q7gb1             SCOP domains
               CATH domains 1q7gB01 B:2-161,B:337-359 NAD(P)-binding Rossmann-like Domain                                                                                                   1q7gB02 B:162-336 Dihydrodipicolinate Reductase; domain 2                                                                                                                      1q7gB01                 CATH domains
           Pfam domains (1) ----------NAD_binding_3-1q7gB01 B:12-143                                                                                                      -------Homoserine_dh-1q7gB03 B:151-353                                                                                                                                                                            ------ Pfam domains (1)
           Pfam domains (2) ----------NAD_binding_3-1q7gB02 B:12-143                                                                                                      -------Homoserine_dh-1q7gB04 B:151-353                                                                                                                                                                            ------ Pfam domains (2)
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhh....eeeeeeeee..eeee...........hhhhhhhh..ee..hhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh..eee....hhhhhhhhhhhh..........eehhhhh.....hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh................hhhhh...hhhhhhhhhh..hhhhhhhhhhhhhh.eeeeeeeeee....eeeeeeeeee..hhhhh.....eeeeeee........eee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HOMOSER_DHGENASE       ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-359 UniProt: 1-359 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                     Transcript 1
                 1q7g B   2 STKVVNVAVIGAGVVGSAFLDQLLAMKSTITYNLVLLAEAERSLISKDFSPLNVGSDWKAALAASTTKTLPLDDLIAHLKTSPKPVILVDNTSSAYIAGFYTKFVENGISIATPNKKAFSSDLATWKALFSNKPTNGFVYHEATVGAGLPIISFLREIIQTGDEVEKIEGIFSGTLSYIFNEFSTSQANDVKFSDVVKVAKKLGYTEPDPRDDLNGLDVARKVTIVGRISGVEVESPTSFPVQSLIPKPLESVKSADEFLEKLSDYDKDLTQLKKEAATENKVLRFIGKVDVATKSVSVGIEKYDYSHPFASLKGSDNVISIKTKRYTNPVVIQGAGAGAAVTAAGVLGDVIKIAQRL 359
                                    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       261       271       281       291       301       311       321       331       341       351

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Dihydrodipicolinate Reductase; domain 2 (182)

Homologous Superfamily: Dihydrodipicolinate Reductase; domain 2 (178)

Baker's yeast (Saccharomyces cerevisiae) (12)

1a	1q7gA02	A:162-336
1b	1q7gB02	B:162-336

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Baker's yeast (Saccharomyces cerevisiae) (13)

2a	1q7gA01	A:2-161,A:337-359
2b	1q7gB01	B:2-161,B:337-359

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DHOM_YEAST | P31116)

molecular function
	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:0004412	homoserine dehydrogenase activity	Catalysis of the reaction: L-homoserine + NADP+ = L-aspartate-4-semialdehyde + NADPH + H+.
	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.
biological process
	GO:0009082	branched-chain amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
	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:0009090	homoserine biosynthetic process	The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid.
	GO:0009097	isoleucine biosynthetic process	The chemical reactions and pathways resulting in the formation of isoleucine, (2R,3R)-2-amino-3-methylpentanoic acid.
	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.

Asymmetric/Biological Unit
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	1q7g
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(no "Related Entries Specified in the PDB File" available for 1Q7G)

Description

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Ligands, Modified Residues, Ions (2, 3)

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