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(-) Description

Title :  DESIGN AND SYNTHESIS OF NEW ENZYMES BASED ON THE LACTATE DEHYDROGENASE FRAMEWORK
 
Authors :  C. R. Dunn, J. J. Holbrook, H. Muirhead
Date :  26 Nov 91  (Deposition) - 31 Oct 93  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase(Choh(D)-Nad+(A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Dunn, H. M. Wilks, D. J. Halsall, T. Atkinson, A. R. Clarke, H. Muirhead, J. J. Holbrook
Design And Synthesis Of New Enzymes Based On The Lactate Dehydrogenase Framework.
Philos. Trans. R. Soc. London, V. 332 177 1991 Ser. B
PubMed-ID: 1678537

(-) Compounds

Molecule 1 - LACTATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.27
    Engineered: YES
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3OXM1Ligand/IonOXAMIC ACID
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3OXM2Ligand/IonOXAMIC ACID
4SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:109 , ASN A:140 , ARG A:171 , HIS A:195 , ALA A:236 , THR A:246 , NAD A:401BINDING SITE FOR RESIDUE SO4 A 402
2AC2SOFTWAREARG A:173 , HIS A:188 , HOH A:430 , HOH A:433 , HOH A:446 , HOH A:450BINDING SITE FOR RESIDUE SO4 A 403
3AC3SOFTWAREARG B:173 , HIS B:188 , HOH B:442 , HOH B:444 , HOH B:462 , HOH B:463BINDING SITE FOR RESIDUE SO4 B 403
4AC4SOFTWAREGLY A:30 , ALA A:31 , VAL A:32 , ASP A:53 , VAL A:54 , MET A:55 , THR A:97 , ALA A:98 , GLY A:99 , ALA A:100 , ARG A:101 , PHE A:122 , ILE A:123 , VAL A:138 , ASN A:140 , SER A:163 , LEU A:167 , HIS A:195 , THR A:246 , ILE A:250 , SO4 A:402 , HOH A:404 , HOH A:411 , HOH A:413 , HOH A:424 , HOH A:429 , HOH A:442 , HOH A:464 , HOH B:425 , HOH B:473BINDING SITE FOR RESIDUE NAD A 401
5AC5SOFTWAREGLY B:30 , ALA B:31 , VAL B:32 , ASP B:53 , VAL B:54 , MET B:55 , THR B:97 , ALA B:98 , GLY B:99 , ALA B:100 , ARG B:101 , ILE B:119 , VAL B:138 , ASN B:140 , SER B:163 , HIS B:195 , THR B:246 , ILE B:250 , OXM B:402 , HOH B:407 , HOH B:414 , HOH B:416 , HOH B:429 , HOH B:441BINDING SITE FOR RESIDUE NAD B 401
6AC6SOFTWAREGLN B:102 , ARG B:109 , ASN B:140 , ARG B:171 , HIS B:195 , ALA B:236 , THR B:246 , NAD B:401BINDING SITE FOR RESIDUE OXM B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 9LDB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:140 -Pro A:141
2Asn B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 9LDB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 9LDB)

(-) Exons   (0, 0)

(no "Exon" information available for 9LDB)

(-) Sequences/Alignments

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
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -d9ldba1 A:1-162 Lactate dehydrogenase                                                                                                                          d9ldba2 A:163-331 Lactate dehydrogenase                                                                                                                                      SCOP domains
               CATH domains -9ldbA01 A:1-164 NAD(P)-binding Rossmann-like Domain                                                                                                              9ldbA02 A:165-331 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.............eeeeee..hhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhh........eeee..........eeeeee..............hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh......eee...hhhhhhhhhhhhhhh......eeeeee.......eee...eee..eee................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....eeeeeeeee.........eeeeeeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                9ldb A    0 xATLKDQLIHNLLKEEHVPHNKITVVGVGAVGMACAISILMKELADEIALVDVMEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSRLVVITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPNCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWILGEHGDSSVPVWSGVNVAGVSLKNLHPELGTDADKEHWKAVHKEVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGLYGIKENVFLSVPCILGQNGISDVVKVTLTPEEEAHLKKSADTLWGIQKELQF  331
                            |        9      ||20|       31        41        51        61        71        81|       92       102||     113       123      132B       142       152       162       172       182       192       202      209D||     218       228       238       248       258       268       278       288       298||     309       319       329  
                            |              16| ||                                                         81|                 103|                       132A|                                                                         209A|||||                                                                                      299|                              
                            0-ACE           18 ||                                                          83                  105                        132B                                                                          209B||||                                                                                       301                              
                                              20|                                                                                                                                                                                        209C|||                                                                                                                        
                                               22                                                                                                                                                                                         209D||                                                                                                                        
                                                                                                                                                                                                                                           210A|                                                                                                                        
                                                                                                                                                                                                                                            210B                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -d9ldbb1 B:1-162 Lactate dehydrogenase                                                                                                                          d9ldbb2 B:163-331 Lactate dehydrogenase                                                                                                                                      SCOP domains
               CATH domains -9ldbB01 B:1-164 NAD(P)-binding Rossmann-like Domain                                                                                                              9ldbB02 B:165-331 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.............eeeeee..hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.........eeee..........eeeeee..............hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh......eee...hhhhhhhhhhhhhhh......eeeeee.......eee...eee..eee................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....eeeeeeeee.........eeeeeeeeee..eeeeeee....hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                9ldb B    0 xATLKDQLIHNLLKEEHVPHNKITVVGVGAVGMACAISILMKELADEIALVDVMEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSRLVVITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPNCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWILGEHGDSSVPVWSGVNVAGVSLKNLHPELGTDADKEHWKAVHKEVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGLYGIKENVFLSVPCILGQNGISDVVKVTLTPEEEAHLKKSADTLWGIQKELQF  331
                            |        9      ||20|       31        41        51        61        71        81|       92       102||     113       123      132B       142       152       162       172       182       192       202      209D||     218       228       238       248       258       268       278       288       298||     309       319       329  
                            0-ACE          16| ||                                                         81|                 103|                       132A|                                                                         209A|||||                                                                                      299|                              
                                            18 ||                                                          83                  105                        132B                                                                          209B||||                                                                                       301                              
                                              20|                                                                                                                                                                                        209C|||                                                                                                                        
                                               22                                                                                                                                                                                         209D||                                                                                                                        
                                                                                                                                                                                                                                           210A|                                                                                                                        
                                                                                                                                                                                                                                            210B
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 9LDB)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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