3D5T - JenaLib

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Title :   CRYSTAL STRUCTURE OF MALATE DEHYDROGENASE FROM BURKHOLDERIA PSEUDOMALLEI

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   16 May 08 (Deposition) - 03 Jun 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.51

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

Keywords :   Ssgcid, Structural Genomics, Niaid, Decode Biostructures, Malate Dehydrogenase, Nad, Oxidoreductase, Tricarboxylic Acid Cycle, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Malate Dehydrogenase From Burkholderia Pseudomallei.
To Be Published
PubMed: search

Molecule 1 - MALATE DEHYDROGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.37
	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	:	MDH, BURPS1710B_A0795
	Organism Scientific	:	BURKHOLDERIA PSEUDOMALLEI
	Organism Taxid	:	320372
	Strain	:	1710B

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC2	SOFTWARE	TRP B:262	BINDING SITE FOR RESIDUE MG B 401

(no "SS Bond" information available for 3D5T)

Asymmetric Unit

No.	Residues
1	Asn A:132	-	Pro A:133
2	Asn B:132	-	Pro B:133
3	Asn C:132	-	Pro C:133
4	Asn D:132	-	Pro D:133

(no "SAP(SNP)/Variant" information available for 3D5T)

(no "PROSITE Motif" information available for 3D5T)

(no "Exon" information available for 3D5T)

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:321
 aligned with MDH_BURP1 | Q3JKE9 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:323
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
            MDH_BURP1     3 KPAKRVAVTGAAGQIAYSLLFRIANGDLLGKDQPVILQLLDLPQAQAAVKGVVMELDDCAFPLLAGVVITDDPKVAFKDADVALLVGARPRSKGMERKDLLSANAEIFTVQGAALNEVASRDVKVLVVGNPANTNAYIAMKSAPDLPKKNFTAMLRLDHNRALSQLAAKSGKPVASIEKLAVWGNHSPTMYPDFRFATAEGESLLKLINDDVWNRDTFIPTVGKRGAAIIEARGLSSAASAANAAIDHVRDWVLGTNGKWVTMGIPSDGSYGIPEDIIYGVPVICENGEYKRVEGLEIDAFSREKMDGTLAELLEERDGVAHL 325
               SCOP domains d3d5ta1 A:3-156 automated matches                                                                                                                         d3d5ta2 A:157-325 automated matches                                                                                                                                       SCOP domains
               CATH domains 3d5tA01 A:3-155 NAD(P)-binding Rossmann-like Domain                                                                                                      3d5tA02 A:156-325 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhh...eeee.......--.hhhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....hhh.eee.hhhhhhhhhhhhhhhhh.hhhhh...eee.......eee.........hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhh....eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d5t A   3 KPAKRVAVTGAAGQIAYSLLFRIANGDLLGKDQPVILQLLDLPQAQAAVKGVVMELDDCAFPLLAGVVITDDPKVAFKDADVALLVGARPRS--MERKDLLSANAEIFTVQGAALNEVASRDVKVLVVGNPANTNAYIAMKSAPDLPKKNFTAMLRLDHNRALSQLAAKSGKPVASIEKLAVWGNHSPTMYPDFRFATAEGESLLKLINDDVWNRDTFIPTVGKRGAAIIEARGLSSAASAANAAIDHVRDWVLGTNGKWVTMGIPSDGSYGIPEDIIYGVPVICENGEYKRVEGLEIDAFSREKMDGTLAELLEERDGVAHL 325
                                    12        22        32        42        52        62        72        82        92 |  |  102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
                                                                                                                      94 97

Chain B from PDB  Type:PROTEIN  Length:321
 aligned with MDH_BURP1 | Q3JKE9 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:323
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
            MDH_BURP1     3 KPAKRVAVTGAAGQIAYSLLFRIANGDLLGKDQPVILQLLDLPQAQAAVKGVVMELDDCAFPLLAGVVITDDPKVAFKDADVALLVGARPRSKGMERKDLLSANAEIFTVQGAALNEVASRDVKVLVVGNPANTNAYIAMKSAPDLPKKNFTAMLRLDHNRALSQLAAKSGKPVASIEKLAVWGNHSPTMYPDFRFATAEGESLLKLINDDVWNRDTFIPTVGKRGAAIIEARGLSSAASAANAAIDHVRDWVLGTNGKWVTMGIPSDGSYGIPEDIIYGVPVICENGEYKRVEGLEIDAFSREKMDGTLAELLEERDGVAHL 325
               SCOP domains d3d5tb1 B:3-156 automated matches                                                                                                                         d3d5tb2 B:157-325 automated matches                                                                                                                                       SCOP domains
               CATH domains 3d5tB01 B:3-155 NAD(P)-binding Rossmann-like Domain                                                                                                      3d5tB02 B:156-325 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhh...eeee.......--.hhhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....hhh.eee.hhhhhhhhhhhhhhhhh.hhh.ee..eee.......eee....ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhh....eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d5t B   3 KPAKRVAVTGAAGQIAYSLLFRIANGDLLGKDQPVILQLLDLPQAQAAVKGVVMELDDCAFPLLAGVVITDDPKVAFKDADVALLVGARPRS--MERKDLLSANAEIFTVQGAALNEVASRDVKVLVVGNPANTNAYIAMKSAPDLPKKNFTAMLRLDHNRALSQLAAKSGKPVASIEKLAVWGNHSPTMYPDFRFATAEGESLLKLINDDVWNRDTFIPTVGKRGAAIIEARGLSSAASAANAAIDHVRDWVLGTNGKWVTMGIPSDGSYGIPEDIIYGVPVICENGEYKRVEGLEIDAFSREKMDGTLAELLEERDGVAHL 325
                                    12        22        32        42        52        62        72        82        92 |  |  102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
                                                                                                                      94 97

Chain C from PDB  Type:PROTEIN  Length:323
 aligned with MDH_BURP1 | Q3JKE9 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:323
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
            MDH_BURP1     3 KPAKRVAVTGAAGQIAYSLLFRIANGDLLGKDQPVILQLLDLPQAQAAVKGVVMELDDCAFPLLAGVVITDDPKVAFKDADVALLVGARPRSKGMERKDLLSANAEIFTVQGAALNEVASRDVKVLVVGNPANTNAYIAMKSAPDLPKKNFTAMLRLDHNRALSQLAAKSGKPVASIEKLAVWGNHSPTMYPDFRFATAEGESLLKLINDDVWNRDTFIPTVGKRGAAIIEARGLSSAASAANAAIDHVRDWVLGTNGKWVTMGIPSDGSYGIPEDIIYGVPVICENGEYKRVEGLEIDAFSREKMDGTLAELLEERDGVAHL 325
               SCOP domains d3d5tc1 C:3-156 automated matches                                                                                                                         d3d5tc2 C:157-325 automated matches                                                                                                                                       SCOP domains
               CATH domains 3d5tC01 C:3-155 NAD(P)-binding Rossmann-like Domain                                                                                                      3d5tC02 C:156-325 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhh....eeee...........hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....hhh.eee.hhhhhhhhhhhhhhhhh.....ee..eee.......eee....ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhh....eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d5t C   3 KPAKRVAVTGAAGQIAYSLLFRIANGDLLGKDQPVILQLLDLPQAQAAVKGVVMELDDCAFPLLAGVVITDDPKVAFKDADVALLVGARPRSKGMERKDLLSANAEIFTVQGAALNEVASRDVKVLVVGNPANTNAYIAMKSAPDLPKKNFTAMLRLDHNRALSQLAAKSGKPVASIEKLAVWGNHSPTMYPDFRFATAEGESLLKLINDDVWNRDTFIPTVGKRGAAIIEARGLSSAASAANAAIDHVRDWVLGTNGKWVTMGIPSDGSYGIPEDIIYGVPVICENGEYKRVEGLEIDAFSREKMDGTLAELLEERDGVAHL 325
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322

Chain D from PDB  Type:PROTEIN  Length:321
 aligned with MDH_BURP1 | Q3JKE9 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:323
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
            MDH_BURP1     3 KPAKRVAVTGAAGQIAYSLLFRIANGDLLGKDQPVILQLLDLPQAQAAVKGVVMELDDCAFPLLAGVVITDDPKVAFKDADVALLVGARPRSKGMERKDLLSANAEIFTVQGAALNEVASRDVKVLVVGNPANTNAYIAMKSAPDLPKKNFTAMLRLDHNRALSQLAAKSGKPVASIEKLAVWGNHSPTMYPDFRFATAEGESLLKLINDDVWNRDTFIPTVGKRGAAIIEARGLSSAASAANAAIDHVRDWVLGTNGKWVTMGIPSDGSYGIPEDIIYGVPVICENGEYKRVEGLEIDAFSREKMDGTLAELLEERDGVAHL 325
               SCOP domains d3d5td1 D:3-156 automated matches                                                                                                                         d3d5td2 D:157-325 automated matches                                                                                                                                       SCOP domains
               CATH domains 3d5tD01 D:3-155 NAD(P)-binding Rossmann-like Domain                                                                                                      3d5tD02 D:156-325 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhhh........eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhh....eeee.......--.hhhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....hhh.eee.hhhhhhhhhhhhhhhhh.hhh.ee..eee.......eee....ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhh....eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d5t D   3 KPAKRVAVTGAAGQIAYSLLFRIANGDLLGKDQPVILQLLDLPQAQAAVKGVVMELDDCAFPLLAGVVITDDPKVAFKDADVALLVGARPRS--MERKDLLSANAEIFTVQGAALNEVASRDVKVLVVGNPANTNAYIAMKSAPDLPKKNFTAMLRLDHNRALSQLAAKSGKPVASIEKLAVWGNHSPTMYPDFRFATAEGESLLKLINDDVWNRDTFIPTVGKRGAAIIEARGLSSAASAANAAIDHVRDWVLGTNGKWVTMGIPSDGSYGIPEDIIYGVPVICENGEYKRVEGLEIDAFSREKMDGTLAELLEERDGVAHL 325
                                    12        22        32        42        52        62        72        82        92 |  |  102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
                                                                                                                      94 97

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: LDH C-terminal domain-like (172)

Superfamily: LDH C-terminal domain-like (172)

Family: automated matches (38)

Protein domain: automated matches (38)

Burkholderia pseudomallei [TaxId: 320372] (1)

1a	d3d5ta2	A:157-325
1b	d3d5tb2	B:157-325
1c	d3d5tc2	C:157-325
1d	d3d5td2	D:157-325

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Burkholderia pseudomallei [TaxId: 320372] (5)

2a	d3d5ta1	A:3-156
2b	d3d5tb1	B:3-156
2c	d3d5tc1	C:3-156
2d	d3d5td1	D:3-156

(no "Pfam Domain" information available for 3D5T)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MDH_BURP1 | Q3JKE9)

molecular function
	GO:0030060	L-malate dehydrogenase activity	Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016615	malate dehydrogenase activity	Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate.
	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.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0006108	malate metabolic process	The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
	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:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

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	Cis Peptide Bonds
		Asn A:132 - Pro A:133	[ RasMol ]
		Asn B:132 - Pro B:133	[ RasMol ]
		Asn C:132 - Pro C:133	[ RasMol ]
		Asn D:132 - Pro D:133	[ RasMol ]

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Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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