3L0D - JenaLib

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Title :   CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BARTONELLA HENSELAE WITH BOUND NAD

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   09 Dec 09 (Deposition) - 29 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Niaid, Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Lyme Disease, Tick-Transmitted Pathogen, Bartonellosis, Als Collaborative Crystallography, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. E. Edwards, J. Abendroth, B. Sankaran, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Glyceraldehyde-3-Phosphate Dehydrogenase From Bartonella Henselae With Bound Nad
To Be Published
PubMed: search

Molecule 1 - GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.2.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	AVA0421
	Gene	:	GAP, BH15080
	Organism Common	:	ROCHALIMAEA HENSELAE
	Organism Scientific	:	BARTONELLA HENSELAE
	Organism Taxid	:	38323

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B
Biological Unit 3 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:9 , PHE A:10 , GLY A:11 , ARG A:12 , ILE A:13 , ASN A:35 , ASP A:36 , CYS A:98 , THR A:99 , GLY A:100 , ILE A:101 , SER A:122 , ALA A:123 , CYS A:153 , ASN A:316 , GLU A:317 , PHE A:320 , HOH A:405 , HOH A:409 , HOH A:410	BINDING SITE FOR RESIDUE NAD A 336
2	AC2	SOFTWARE	THR A:191 , MET A:192 , GLY B:11 , ARG B:12 , ILE B:13 , ASP B:36 , ARG B:80 , CYS B:98 , THR B:99 , GLY B:100 , ILE B:101 , SER B:122 , ALA B:123 , CYS B:153 , ASN B:316	BINDING SITE FOR RESIDUE NAD B 336

(no "SS Bond" information available for 3L0D)

(no "Cis Peptide Bond" information available for 3L0D)

(no "SAP(SNP)/Variant" information available for 3L0D)

(no "PROSITE Motif" information available for 3L0D)

(no "Exon" information available for 3L0D)

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:332
 aligned with Q8L201_BARHN | Q8L201 from UniProtKB/TrEMBL  Length:335

    Alignment length:335
                                    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     
         Q8L201_BARHN     1 MSVRVAINGFGRIGRNILRAIIESGRQDIEVVALNDLGSVETNAHLLRYDSVHGCFPGTVQVVGDAIDIGSSLIKVFAERDPAQLPWKALDIDIALECTGIFTARDKASAHLDAGAKRVLVSAPSEGADLTVVYGVNHQFLSKEHHVISNASCTTNCLAPVAQVLHNTVGIEKGFMTTIHSYTGDQPVLDTMHRDLYRARAAALSMIPTSTGAAKAVGLVLPELKGLLDGVSIRVPTPNVSVVDLTFTAKRSTTIEEINTAIRTAAQGSLKGILDYTDEKLVSCDFNHNPHSAIFHNDQTKVIDGQLCRVLVWYDNEWGFSNRMCDTAVAFAKTI 335
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3l0dA01 A:1-151,A:317-335 NAD(P)-binding Rossmann-like Domain                                                                                          3l0dA02 A:152-316 Dihydrodipicolinate Reductase; domain 2                                                                                                            3l0dA01             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhee...ee.....eee..eee.---.eeee...hhhhh........eeee......hhhhhhhhhhh...eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee.........................eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheee...eeeeeeee..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0d A   1 MSVRVAINGFGRIGRNILRAIIESGRQDIEVVALNDLGSVETNAHLLRYDSVHGCFPGTVQVVGDAIDI---LIKVFAERDPAQLPWKALDIDIALECTGIFTARDKASAHLDAGAKRVLVSAPSEGADLTVVYGVNHQFLSKEHHVISNASCTTNCLAPVAQVLHNTVGIEKGFMTTIHSYTGDQPVLDTMHRDLYRARAAALSMIPTSTGAAKAVGLVLPELKGLLDGVSIRVPTPNVSVVDLTFTAKRSTTIEEINTAIRTAAQGSLKGILDYTDEKLVSCDFNHNPHSAIFHNDQTKVIDGQLCRVLVWYDNEWGFSNRMCDTAVAFAKTI 335
                                    10        20        30        40        50        60        |-  |     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     
                                                                                               69  73

Chain B from PDB  Type:PROTEIN  Length:332
 aligned with Q8L201_BARHN | Q8L201 from UniProtKB/TrEMBL  Length:335

    Alignment length:335
                                    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     
         Q8L201_BARHN     1 MSVRVAINGFGRIGRNILRAIIESGRQDIEVVALNDLGSVETNAHLLRYDSVHGCFPGTVQVVGDAIDIGSSLIKVFAERDPAQLPWKALDIDIALECTGIFTARDKASAHLDAGAKRVLVSAPSEGADLTVVYGVNHQFLSKEHHVISNASCTTNCLAPVAQVLHNTVGIEKGFMTTIHSYTGDQPVLDTMHRDLYRARAAALSMIPTSTGAAKAVGLVLPELKGLLDGVSIRVPTPNVSVVDLTFTAKRSTTIEEINTAIRTAAQGSLKGILDYTDEKLVSCDFNHNPHSAIFHNDQTKVIDGQLCRVLVWYDNEWGFSNRMCDTAVAFAKTI 335
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3l0dB01 B:1-151,B:317-335 NAD(P)-binding Rossmann-like Domain                                                                                          3l0dB02 B:152-316 Dihydrodipicolinate Reductase; domain 2                                                                                                            3l0dB01             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhee...ee.....ee...eee.---.eeee...hhhhh.hhhhh..eeee......hhhhhhhhhhh...eeee...............hhhhh.....eee....hhhhhhhhhhhhhhhhheeeeeeeeeee.........................eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheee...eeeeeeee..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0d B   1 MSVRVAINGFGRIGRNILRAIIESGRQDIEVVALNDLGSVETNAHLLRYDSVHGCFPGTVQVVGDAIDI---LIKVFAERDPAQLPWKALDIDIALECTGIFTARDKASAHLDAGAKRVLVSAPSEGADLTVVYGVNHQFLSKEHHVISNASCTTNCLAPVAQVLHNTVGIEKGFMTTIHSYTGDQPVLDTMHRDLYRARAAALSMIPTSTGAAKAVGLVLPELKGLLDGVSIRVPTPNVSVVDLTFTAKRSTTIEEINTAIRTAAQGSLKGILDYTDEKLVSCDFNHNPHSAIFHNDQTKVIDGQLCRVLVWYDNEWGFSNRMCDTAVAFAKTI 335
                                    10        20        30        40        50        60        |-  |     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     
                                                                                               69  73

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 3L0D)

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	3l0dA02	A:152-316
1b	3l0dB02	B:152-316

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	3l0dA01	A:1-151,A:317-335
2b	3l0dB01	B:1-151,B:317-335

(no "Pfam Domain" information available for 3L0D)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8L201_BARHN | Q8L201)

molecular function
	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:0004365	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity	Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
biological process
	GO:0006006	glucose metabolic process	The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
	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.

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3doc	GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BRUCELLA MELITENSIS WITH BOUND NAD
3gnq	GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BURKHOLDERIA PSEUDOMALLEI WITH BOUND NAD RELATED ID: BAHEA.00617.A RELATED DB: TARGETDB

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