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(-) Description

Title :  CRYSTAL STRUCTURE OF L-LACTATE DEHYDROGENASE FROM BACILLUS SELENITIREDUCENS MLS10, NYSGRC TARGET 029814.
 
Authors :  V. N. Malashkevich, R. Bhosle, R. Toro, B. Hillerich, A. Gizzi, S. Garfo A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. Chamala, S. L A. Celikgil, G. Villegas, B. Evans, J. Love, A. Fiser, K. Khafizov, R. S J. B. Bonanno, S. C. Almo, New York Structural Genomics Research Consortium (Nysgrc)
Date :  03 Aug 13  (Deposition) - 21 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Structural Genomics, Protein Structure Initiative, L-Lactate Dehydrogenase, Nysgrc, Psi-Biology, New York Structural Genomics Research Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Bhosle, R. Toro, B. Hillerich, A. Gizzi, S. Garforth, A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. Chamala, S. Lim, A. Celikgil, G. Villegas, B. Evans, J. Love, A. Fiser, K. Khafizov, R. Seidel, J. B. Bonanno, S. C. Almo
Crystal Structure Of L-Lactate Dehydrogenase From Bacillus Selenitireducens Mls10, Nysgrc Target 029814.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LDH, BSEL_2311
    Organism Scientific: BACILLUS SELENITIREDUCENS
    Organism Taxid: 439292
    Strain: MLS10
    Synonym: L-LDH

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 28)

Asymmetric Unit (3, 28)
No.NameCountTypeFull Name
1MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE20Mod. Amino AcidSELENOMETHIONINE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 56)
No.NameCountTypeFull Name
1MPD12Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE40Mod. Amino AcidSELENOMETHIONINE
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:155 , HIS A:170 , TYR A:172 , HOH A:505 , HOH A:520 , HOH A:539 , ASN B:168 , HIS B:170 , GLY B:191 , SER B:192 , HOH B:508BINDING SITE FOR RESIDUE PO4 A 401
2AC2SOFTWAREMSE A:48 , ASN A:51 , HIS A:52 , HOH A:603 , PHE B:156 , ASN B:217BINDING SITE FOR RESIDUE MPD A 402
3AC3SOFTWAREASP A:212 , ASP B:266 , ASP B:268 , HOH B:749 , HOH B:750BINDING SITE FOR RESIDUE MPD A 403
4AC4SOFTWAREGLY A:81 , ILE A:100 , HOH A:536 , HOH A:630 , HOH A:777 , PRO B:312 , PHE B:314 , HOH B:681BINDING SITE FOR RESIDUE MPD A 404
5AC5SOFTWAREASN A:168 , HIS A:170 , GLY A:191 , SER A:192 , ARG B:155 , HIS B:170 , TYR B:172 , HOH B:506 , HOH B:511 , HOH B:513 , HOH B:589BINDING SITE FOR RESIDUE PO4 B 401
6AC6SOFTWAREPHE A:156 , ASN A:217 , MSE B:48 , ASN B:51 , HIS B:52 , HOH B:565BINDING SITE FOR RESIDUE MPD B 402
7AC7SOFTWARELEU A:38 , ASP A:39 , ALA B:98 , ASN B:99 , LYS B:102 , HOH B:777BINDING SITE FOR RESIDUE MPD B 403
8AC8SOFTWARETRP B:185 , ASN B:208 , ASP B:212 , HOH B:595 , HOH B:675BINDING SITE FOR RESIDUE MPD B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M1Q)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:122 -Pro A:123
2Asn B:122 -Pro B:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M1Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M1Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4M1Q)

(-) 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:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4m1qa1 A:3-144 automated matches                                                                                                             d4m1qa2 A:145-314 automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh.hhhhh...eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m1q A   3 TKTSRVVIIGTGAVGSSYAFSmINQNVTDEmVLIDLDKRKTEGDAmDLNHGIPFGAPTKVWAGDYGDCKSADIVVITAGAAQKPGETRLDLVEKNANIFKGIVDQVmGSGFNGIFIIATNPVDVLAYATWKFSGLPKERVIGSGTILDTARFRFLLSEYFDIDVRNIHGYImGEHGDTELPVWSQTRIGSEPISRYmDKYKPDGSNKDLDEIFVNVRDAAYHIIERKGATHYAIAmGLARLTKAILRNEQSILTVSTLmEGEYDLDDVYIGVPAIVSQKGVERAIEIDLNDEEmKKLHHSSNTLKDVmKPIF 314
                                    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  
                                                24-MSE   33-MSE         48-MSE                                                      109-MSE                                                          174-MSE                  199-MSE                                238-MSE                261-MSE                            296-MSE       310-MSE


Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4m1qb1 B:4-144 automated matches                                                                                                         d4m1qb2 B:145-315 automated matches                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh.hhhhh...eeee.hhhhhh...eeee.......hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m1q B   4 KTSRVVIIGTGAVGSSYAFSmINQNVTDEmVLIDLDKRKTEGDAmDLNHGIPFGAPTKVWAGDYGDCKSADIVVITAGAAGETRLDLVEKNANIFKGIVDQVmGSGFNGIFIIATNPVDVLAYATWKFSGLPKERVIGSGTILDTARFRFLLSEYFDIDVRNIHGYImGEHGDTELPVWSQTRIGSEPISRYmDKYKPDGSNKDLDEIFVNVRDAAYHIIERKGATHYAIAmGLARLTKAILRNEQSILTVSTLmEGEYDLDDVYIGVPAIVSQKGVERAIEIDLNDEEmKKLHHSSNTLKDVmKPIFD 315
                                    13        23|       33        43    |   53        63        73        83|       96       106  |    116       126       136       146       156       166       176       186       196  |    206       216       226       236 |     246       256    |  266       276       286       296       306   |     
                                               24-MSE   33-MSE         48-MSE                             83|                   109-MSE                                                          174-MSE                  199-MSE                                238-MSE                261-MSE                            296-MSE       310-MSE 
                                                                                                           87
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "CATH Domain" information available for 4M1Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M1Q)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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