4MDH
REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT 2.5-ANGSTROMS RESOLUTION
External Resource: Annotation
- Domain Annotation: SCOP/SCOPe Classification
- Domain Annotation: SCOP2 Classification
- Domain Annotation: ECOD Classification
- Domain Annotation: CATH
- Protein Family Annotation
- Gene Ontology: Gene Product Annotation
- InterPro: Protein Family Classification
- Protein Modification Annotation
- Structure Motif: Primary M-CSA Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d4mdha1 | Alpha and beta proteins (a/b) | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | LDH N-terminal domain-like | Malate dehydrogenase | pig (Sus scrofa ) [TaxId: 9823 ], | SCOPe (2.08) |
A | d4mdha2 | Alpha and beta proteins (a+b) | LDH C-terminal domain-like | LDH C-terminal domain-like | Lactate & malate dehydrogenases, C-terminal domain | Malate dehydrogenase | pig (Sus scrofa ) [TaxId: 9823 ], | SCOPe (2.08) |
B | d4mdhb1 | Alpha and beta proteins (a/b) | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | LDH N-terminal domain-like | Malate dehydrogenase | pig (Sus scrofa ) [TaxId: 9823 ], | SCOPe (2.08) |
B | d4mdhb2 | Alpha and beta proteins (a+b) | LDH C-terminal domain-like | LDH C-terminal domain-like | Lactate & malate dehydrogenases, C-terminal domain | Malate dehydrogenase | pig (Sus scrofa ) [TaxId: 9823 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | Ldh_1_C_3 | e4mdhA3 | A: a+b complex topology | X: LDH C-terminal domain-like (From Topology) | H: LDH C-terminal domain-like (From Topology) | T: LDH C-terminal domain-like | F: Ldh_1_C_3 | ECOD (1.6) |
A | Ldh_1_N | e4mdhA2 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: Ldh_1_N | ECOD (1.6) |
B | Ldh_1_C_3 | e4mdhB3 | A: a+b complex topology | X: LDH C-terminal domain-like (From Topology) | H: LDH C-terminal domain-like (From Topology) | T: LDH C-terminal domain-like | F: Ldh_1_C_3 | ECOD (1.6) |
B | Ldh_1_N | e4mdhB2 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Rossmann-related | T: NAD(P)-binding Rossmann-fold domains | F: Ldh_1_N | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.40.50.720 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | NAD(P)-binding Rossmann-like Domain | CATH (4.3.0) |
A | 3.90.110.10 | Alpha Beta | Alpha-Beta Complex | L-2-Hydroxyisocaproate Dehydrogenase | Chain A, domain 2 | CATH (4.3.0) |
B | 3.40.50.720 | Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | NAD(P)-binding Rossmann-like Domain | CATH (4.3.0) |
B | 3.90.110.10 | Alpha Beta | Alpha-Beta Complex | L-2-Hydroxyisocaproate Dehydrogenase | Chain A, domain 2 | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF02866 | lactate/malate dehydrogenase, alpha/beta C-terminal domain (Ldh_1_C) | lactate/malate dehydrogenase, alpha/beta C-terminal domain | L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the in ... | Domain | |
PF00056 | lactate/malate dehydrogenase, NAD binding domain (Ldh_1_N) | lactate/malate dehydrogenase, NAD binding domain | L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the in ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR015955 | Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal | Homologous Superfamily | |
IPR001252 | Malate dehydrogenase, active site | Active Site | |
IPR001557 | L-lactate/malate dehydrogenase | Family | |
IPR011274 | Malate dehydrogenase, NAD-dependent, cytosolic | Family | |
IPR001236 | Lactate/malate dehydrogenase, N-terminal | Domain | |
IPR010945 | Malate dehydrogenase, type 2 | Family | |
IPR036291 | NAD(P)-binding domain superfamily | Homologous Superfamily | |
IPR022383 | Lactate/malate dehydrogenase, C-terminal | Domain |
Protein Modification Annotation
Modified Residue(s) | ||
---|---|---|
Chain | Residue(s) | Description |
ACE | AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 :  N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359 | : 
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
malate dehydrogenase (type 2) M-CSA #526 | Malate dehydrogenase catalysis the readily reversible dehydrogenation of malate to oxaloacetate. As the activated cofactor/substrate complex has a net negative charge, a positive counter-charge is provided by conserved arginines in the active site. By this mechanism, malate dehydrogenase uses charge balancing to achieve fivefold orders of magnitude in discrimination between potential substrates. | Defined by 2 residues: ASP:A-159 [auth A-158]HIS:A-187 [auth A-186] | EC: 1.1.1.37 (PDB Primary Data) |