2P9C - JenaLib

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Title :   CRYSTAL STRUCTURE OF SERINE BOUND G336V MUTANT OF E.COLI PHOSPHOGLYCERATE DEHYDROGENASE

Authors :   S. Dey, J. C. Sacchettini

Date :   24 Mar 07 (Deposition) - 24 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.46

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

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

Reference :   S. Dey, Z. Hu, X. L. Xu, J. C. Sacchettini, G. A. Grant
The Effect Of Hinge Mutations On Effector Binding And Domai Rotation In Escherichia Coli D-3-Phosphoglycerate Dehydrogenase
J. Biol. Chem. V. 282 18418 2007
PubMed-ID: 17459882 | Reference-DOI: 10.1074/JBC.M701174200

Molecule 1 - D-3-PHOSPHOGLYCERATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.95
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC99
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SERA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PGDH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	NAI	2	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2	SER	2	Mod. Amino Acid	SERINE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	NAI	4	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2	SER	4	Mod. Amino Acid	SERINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:84 , PHE A:106 , VAL A:112 , GLY A:158 , TYR A:159 , GLY A:160 , HIS A:161 , ILE A:162 , TYR A:180 , ASP A:181 , ILE A:182 , LYS A:185 , HIS A:210 , VAL A:211 , PRO A:212 , SER A:216 , MET A:220 , ALA A:238 , SER A:239 , ARG A:240 , ASP A:264 , HIS A:292 , GLY A:294 , GLY A:295 , HOH A:569	BINDING SITE FOR RESIDUE NAI A 450
2	AC2	SOFTWARE	ILE B:84 , PHE B:106 , ASN B:108 , VAL B:112 , TYR B:159 , GLY B:160 , HIS B:161 , ILE B:162 , ASP B:181 , ILE B:182 , LYS B:185 , HIS B:210 , VAL B:211 , PRO B:212 , SER B:216 , THR B:217 , MET B:220 , ALA B:238 , SER B:239 , ARG B:240 , ASP B:264 , HIS B:292 , GLY B:294 , GLY B:295	BINDING SITE FOR RESIDUE NAI B 550
3	AC3	SOFTWARE	HIS A:344 , ASN A:346 , ARG A:347 , PRO A:348 , GLY A:349 , LEU A:351 , LEU A:370 , HOH A:563 , ASN B:364 , ILE B:365	BINDING SITE FOR RESIDUE SER A 451
4	AC4	SOFTWARE	ASN A:364 , ILE A:365 , HIS B:344 , ASN B:346 , ARG B:347 , GLY B:349 , LEU B:351 , LEU B:370	BINDING SITE FOR RESIDUE SER A 551

(no "SS Bond" information available for 2P9C)

Asymmetric Unit

No.	Residues
1	Leu B:6	-	Glu B:7

(no "SAP(SNP)/Variant" information available for 2P9C)

Asymmetric Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	SERA_ECOLI	154-181	2	A:154-181 B:154-181
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	SERA_ECOLI	200-222	2	A:200-222 B:200-222
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	SERA_ECOLI	229-245	2	A:229-245 B:229-245
4	ACT	PS51671	ACT domain profile.	SERA_ECOLI	339-410	2	A:339-410 B:339-410

Biological Unit 1 (4, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	SERA_ECOLI	154-181	4	A:154-181 B:154-181
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	SERA_ECOLI	200-222	4	A:200-222 B:200-222
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	SERA_ECOLI	229-245	4	A:229-245 B:229-245
4	ACT	PS51671	ACT domain profile.	SERA_ECOLI	339-410	4	A:339-410 B:339-410

(no "Exon" information available for 2P9C)

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:405
 aligned with SERA_ECOLI | P0A9T0 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:405
                                    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       305       315       325       335       345       355       365       375       385       395       405     
           SERA_ECOLI     6 LEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410
               SCOP domains -d2p9ca2 A:7-107,A:296-326 Phosphoglycerate dehydrogenase                                             d2p9ca1 A:108-295 Phosphoglycerate dehydrogenase                                                                                                                                            d2p9ca2 A:7-107,A:296-326      d2p9ca3 A:327-410 Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain     SCOP domains
               CATH domains 2p9cA01 A:6-108,A:298-326 NAD(P)-binding Rossmann-like Domain                                          2p9cA02 A:109-297 NAD(P)-binding Rossmann-like Domain                                                                                                                                        2p9cA01 A:6-108,A:298-326    -2p9cA03 A:328-409  [code=3.30.70.260, no name defined]                            - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eee....hhhhhhhhhhh....eee.....hhhhhhhhh....eeee......hhhhhhhh................hhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeee..hhhhhhhhhhhhhh..eeeee...........ee..hhhhhhhhh.eeee............hhhhhhhh...eeeee.......hhhhhhhhhhh..eeeeee...............hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh..................eeeeeeee...hhhhhhhhhhhhh..eeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhh...eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        ------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D---------------------------------------------------------------------------------------------ACT  PDB: A:339-410 UniProt: 339-410                                     PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p9c A   6 LEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGAFAIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALADALASKHLAGAAIDVFPTEPATNSDPFTSPLAEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHVGRRLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410
                                    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       305       315       325       335       345       355       365       375       385       395       405

Chain B from PDB  Type:PROTEIN  Length:405
 aligned with SERA_ECOLI | P0A9T0 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:405
                                    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       305       315       325       335       345       355       365       375       385       395       405     
           SERA_ECOLI     6 LEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410
               SCOP domains -d2p9cb2 B:7-107,B:296-326 Phosphoglycerate dehydrogenase                                             d2p9cb1 B:108-295 Phosphoglycerate dehydrogenase                                                                                                                                            d2p9cb2 B:7-107,B:296-326      d2p9cb3 B:327-410 Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain     SCOP domains
               CATH domains 2p9cB01 B:6-108,B:298-326 NAD(P)-binding Rossmann-like Domain                                          2p9cB02 B:109-297 NAD(P)-binding Rossmann-like Domain                                                                                                                                        2p9cB01 B:6-108,B:298-326    -2p9cB03 B:328-409  [code=3.30.70.260, no name defined]                            - CATH domains
           Pfam domains (1) -------2-Hacid_dh-2p9cB03 B:13-326                                                                                                                                                                                                                                                                                               ------------ACT-2p9cB01 B:339-402                                           -------- Pfam domains (1)
           Pfam domains (2) -------2-Hacid_dh-2p9cB04 B:13-326                                                                                                                                                                                                                                                                                               ------------ACT-2p9cB02 B:339-402                                           -------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------2-Hacid_dh_C-2p9cB05 B:117-294                                                                                                                                                    -------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------2-Hacid_dh_C-2p9cB06 B:117-294                                                                                                                                                    -------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .......eee....hhhhhhhhhhh....eee.....hhhhhhhhhh...eeee......hhhhhhhh................hhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.................eeeee..hhhhhhhhhhhhhh..eeeee...........ee..hhhhhhhhh.eeee............hhhhhh.....eeeee.......hhhhhhhhhhh..eeeeee...............hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh..................eeeeeeee...hhhhhhhhhhhh...eeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhh...eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        ------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D---------------------------------------------------------------------------------------------ACT  PDB: B:339-410 UniProt: 339-410                                     PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p9c B   6 LEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGAFAIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALADALASKHLAGAAIDVFPTEPATNSDPFTSPLAEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHVGRRLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410
                                    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       305       315       325       335       345       355       365       375       385       395       405

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.260, no name defined] (34)

Escherichia coli. Organism_taxid: 562. (7)

1a	2p9cA03	A:328-409
1b	2p9cB03	B:328-409

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

Topology: Rossmann fold (7312)

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

Escherichia coli. Organism_taxid: 562. (48)

2a	2p9cA02	A:109-297
2b	2p9cA01	A:6-108,A:298-326
2c	2p9cB01	B:6-108,B:298-326
2d	2p9cB02	B:109-297

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ACT (34)

Family: ACT (19)

Escherichia coli (strain K12) (5)

1a	ACT-2p9cB01	B:339-402
1b	ACT-2p9cB02	B:339-402

Clan: Form_Glyc_dh (56)

Family: 2-Hacid_dh (21)

Escherichia coli (strain K12) (5)

2a	2-Hacid_dh-2p9cB03	B:13-326
2b	2-Hacid_dh-2p9cB04	B:13-326

Clan: NADP_Rossmann (1239)

Family: 2-Hacid_dh_C (23)

Escherichia coli (strain K12) (5)

3a	2-Hacid_dh_C-2p9cB05	B:117-294
3b	2-Hacid_dh_C-2p9cB06	B:117-294

Asymmetric Unit(hide GO term definitions)

Chain A,B (SERA_ECOLI | P0A9T0)

molecular function
	GO:0047545	2-hydroxyglutarate dehydrogenase activity	Catalysis of the reaction: (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor.
	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:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	GO:0004617	phosphoglycerate dehydrogenase activity	Catalysis of the reaction: 3-phosphoglycerate + NAD+ = 3-phosphohydroxypyruvate + NADH + H+.
	GO:0070905	serine binding	Interacting selectively and non-covalently with 2-amino-3-hydroxypropanoic acid.
biological process
	GO:0006564	L-serine biosynthetic process	The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
	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: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: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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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