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Title :   CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE REDUCTASE FROM BARTONELLA HENSELAE AT 2.0A RESOLUTION

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   04 Aug 09 (Deposition) - 11 Aug 09 (Release) - 01 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Ssgcid, Sbri, Decode Biostructures, Niaid, Bartonella Henselae, Dihydrodipicolinate Reductase, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lysine Biosynthesis, Nadp, Oxidoreductase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. R. Cala, M. T. Nadeau, J. Abendroth, B. L. Staker, A. R. Reers, A. W. Weatherhead, R. C. Dobson, P. J. Myler, A. O. Hudson
The Crystal Structure Of Dihydrodipicolinate Reductase From The Human-Pathogenic Bacterium Bartonella Henselae Strain Houston-1 At 2. 3 Angstrom Resolution.
Acta Crystallogr F Struct V. 72 885 2016 Biol Commun
PubMed-ID: 27917836 | Reference-DOI: 10.1107/S2053230X16018525

Molecule 1 - DIHYDRODIPICOLINATE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.3.1.26
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DAPB, BH12440
	Organism Common	:	ROCHALIMAEA HENSELAE
	Organism Scientific	:	BARTONELLA HENSELAE
	Organism Taxid	:	38323
	Strain	:	HOUSTON-1
	Synonym	:	DHPR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	NA	2	Ligand/Ion	SODIUM ION
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4	UNX	4	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4	UNX	8	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:20 , ARG A:23 , VAL A:26 , HOH A:459 , HOH A:460	BINDING SITE FOR RESIDUE NA A 301
2	AC2	SOFTWARE	HIS A:155 , LYS A:158 , HOH A:374	BINDING SITE FOR RESIDUE CL A 302
3	AC3	SOFTWARE	GLY A:7 , ASN A:9 , GLY A:10 , ARG A:11 , MET A:12 , ARG A:34 , PHE A:74 , SER A:75 , GLN A:76 , TYR A:83 , GLY A:97 , THR A:99 , SER A:121 , GLY A:122 , ASN A:123 , MET A:124 , LYS A:158 , ASP A:160 , PHE A:238 , HOH A:280 , HOH A:282 , HOH A:306 , HOH A:314 , HOH A:349 , HOH A:379 , HOH A:393 , HOH A:397 , HOH A:425 , HOH A:444 , HOH A:454 , HOH A:474	BINDING SITE FOR RESIDUE NAP A 300
4	AC4	SOFTWARE	ILE B:20 , ARG B:23 , VAL B:26 , HOH B:332 , HOH B:481 , HOH B:494	BINDING SITE FOR RESIDUE NA B 301
5	AC5	SOFTWARE	ALA B:8 , ASN B:9 , VAL B:33 , ARG B:34 , HOH B:416	BINDING SITE FOR RESIDUE CL B 302

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

Asymmetric Unit

No.	Residues
1	Ser A:161	-	Pro A:162
2	Gly A:264	-	Leu A:265
3	Ser B:161	-	Pro B:162

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAPB	PS01298	Dihydrodipicolinate reductase signature.	DAPB_BARHE	149-166	2	A:149-166 B:149-166

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAPB	PS01298	Dihydrodipicolinate reductase signature.	DAPB_BARHE	149-166	4	A:149-166 B:149-166

(no "Exon" information available for 3IJP)

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
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Chain A from PDB  Type:PROTEIN  Length:266
 aligned with DAPB_BARHE | Q6G2G3 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:266
                             1                                                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259      
           DAPB_BARHE     - -MRLTVVGANGRMGRELITAIQRRKDVELCAVLVRKGSSFVDKDASILIGSDFLGVRITDDPESAFSNTEGILDFSQPQASVLYANYAAQKSLIHIIGTTGFSKTEEAQIADFAKYTTIVKSGNMSLGVNLLANLVKRAAKALDDDFDIEIYEMHHANKVDSPSGTALLLGQAAAEGRNIMLKNVSVNGRSGHTGKREKGTIGFACSRGGTVIGDHSITFAGENERIVLSHIAQERSIFANGALKAALWAKNHENGLYSMLDVLGL 265
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ijpA01 A:0-125,A:234-265 NAD(P)-binding Rossmann-like Domain                                                                 3ijpA02 A:126-233 Dihydrodipicolinate Reductase; domain 2                                                   3ijpA01 A:0-125,A:234-265        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhh...eeeeee...........hhhhhh...........hhhhhh....eeee..hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhhhh..hhhhheee.hhhh........eeeeeee.....eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhh....eeehhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------DAPB              --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ijp A   0 SMRLTVVGANGRMGRELITAIQRRKDVELCAVLVRKGSSFVDKDASILIGSDFLGVRITDDPESAFSNTEGILDFSQPQASVLYANYAAQKSLIHIIGTTGFSKTEEAQIADFAKYTTIVKSGNMSLGVNLLANLVKRAAKALDDDFDIEIYEMHHANKVDSPSGTALLLGQAAAEGRNIMLKNVSVNGRSGHTGKREKGTIGFACSRGGTVIGDHSITFAGENERIVLSHIAQERSIFANGALKAALWAKNHENGLYSMLDVLGL 265
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259

Chain B from PDB  Type:PROTEIN  Length:267
 aligned with DAPB_BARHE | Q6G2G3 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:267
                             1                                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       
           DAPB_BARHE     - -MRLTVVGANGRMGRELITAIQRRKDVELCAVLVRKGSSFVDKDASILIGSDFLGVRITDDPESAFSNTEGILDFSQPQASVLYANYAAQKSLIHIIGTTGFSKTEEAQIADFAKYTTIVKSGNMSLGVNLLANLVKRAAKALDDDFDIEIYEMHHANKVDSPSGTALLLGQAAAEGRNIMLKNVSVNGRSGHTGKREKGTIGFACSRGGTVIGDHSITFAGENERIVLSHIAQERSIFANGALKAALWAKNHENGLYSMLDVLGLN 266
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ijpB01 B:0-125,B:234-266 NAD(P)-binding Rossmann-like Domain                                                                 3ijpB02 B:126-233 Dihydrodipicolinate Reductase; domain 2                                                   3ijpB01 B:0-125,B:234-266         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhh...eeeeee............hhhhhh..........hhhhhh....eeee..hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhhhh..hhhhheee.hhhh........eeeeeee.....eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhh....eeehhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------DAPB              ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ijp B   0 SMRLTVVGANGRMGRELITAIQRRKDVELCAVLVRKGSSFVDKDASILIGSDFLGVRITDDPESAFSNTEGILDFSQPQASVLYANYAAQKSLIHIIGTTGFSKTEEAQIADFAKYTTIVKSGNMSLGVNLLANLVKRAAKALDDDFDIEIYEMHHANKVDSPSGTALLLGQAAAEGRNIMLKNVSVNGRSGHTGKREKGTIGFACSRGGTVIGDHSITFAGENERIVLSHIAQERSIFANGALKAALWAKNHENGLYSMLDVLGLN 266
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259

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 3IJP)

Asymmetric 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)

Rochalimaea henselae (Bartonella henselae) (2)

1a	3ijpA02	A:126-233
1b	3ijpB02	B:126-233

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

Topology: Rossmann fold (7312)

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

Rochalimaea henselae (Bartonella henselae) (2)

2a	3ijpB01	B:0-125,B:234-266
2b	3ijpA01	A:0-125,A:234-265

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (DAPB_BARHE | Q6G2G3)

molecular function
	GO:0008839	4-hydroxy-tetrahydrodipicolinate reductase	Catalysis of the reaction: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + 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: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:0016726	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	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: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: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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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		Ser A:161 - Pro A:162	[ RasMol ]
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Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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