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(-) Description

Title :  CRYSTAL STRUCTURE OF NADP-DEPENDENT 2-HYDROXYACID DEHYDROGENASE FROM SINORHIZOBIUM MELILOTI IN COMPLEX WITH 2'-PHOSPHO-ADP-RIBOSE
 
Authors :  I. G. Shabalin, O. A. Gasiorowska, K. B. Handing, J. Bonanno, J. Kutner, W. Minor, New York Structural Genomics Research Consortium (N
Date :  29 Mar 16  (Deposition) - 13 Apr 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  2-Hydroxyacid Dehydrogenase, Nadp, Nysgrc, Structural Genomics, Psi- Biology, New York Structural Genomics Research Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. G. Shabalin, O. A. Gasiorowska, K. B. Handing, J. Bonanno, J. Kutner S. C. Almo, W. Minor
Crystal Structure Of Nadp-Dependent 2-Hydroxyacid Dehydrogenase From Sinorhizobium Meliloti In Complex With 2'-Phospho-Adp-Ribose
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2-HYDROXYACID DEHYDROGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGC-HIS
    Expression System Strain: BL21 (DE3) RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMC04462
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: RHIZOBIUM MELILOTI (STRAIN 1021)
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1A2R4Ligand/Ion[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYLDIHYDROGEN DIPHOSPHATE
2ACT3Ligand/IonACETATE ION
3CL7Ligand/IonCHLORIDE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1A2R2Ligand/Ion[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYLDIHYDROGEN DIPHOSPHATE
2ACT2Ligand/IonACETATE ION
3CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1A2R2Ligand/Ion[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYLDIHYDROGEN DIPHOSPHATE
2ACT1Ligand/IonACETATE ION
3CL-1Ligand/IonCHLORIDE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:95 , THR A:285 , ALA A:288 , ARG C:141binding site for residue ACT A 401
02AC2SOFTWAREASN A:13 , ARG A:286 , HOH A:633binding site for residue CL A 402
03AC3SOFTWAREPHE A:148 , LEU A:150 , GLY A:151 , ARG A:152 , ILE A:153 , THR A:172 , ARG A:173 , THR A:174 , ILE A:200 , PRO A:202 , SER A:206 , THR A:207 , VAL A:228 , GLY A:229 , ARG A:230 , HOH A:506 , HOH A:519 , HOH A:532 , HOH A:560 , HOH A:570binding site for residue A2R A 403
04AC4SOFTWAREVAL B:95 , THR B:285 , HOH B:571binding site for residue ACT B 401
05AC5SOFTWAREASN B:13 , ARG B:286 , HOH B:583binding site for residue CL B 402
06AC6SOFTWAREHIS B:277 , A2R B:404binding site for residue CL B 403
07AC7SOFTWARELEU B:150 , GLY B:151 , ARG B:152 , ILE B:153 , THR B:172 , ARG B:173 , THR B:174 , ILE B:200 , PRO B:202 , SER B:206 , THR B:207 , ARG B:230 , CL B:403 , HOH B:509 , HOH B:557 , HOH B:581 , HOH B:582binding site for residue A2R B 404
08AC8SOFTWAREARG A:141 , VAL C:95 , THR C:285 , ALA C:288binding site for residue ACT C 401
09AC9SOFTWAREASN C:13 , ARG C:286 , HOH C:625binding site for residue CL C 402
10AD1SOFTWAREARG C:230 , HIS C:277 , A2R C:404binding site for residue CL C 403
11AD2SOFTWARELEU C:150 , GLY C:151 , ARG C:152 , ILE C:153 , THR C:172 , ARG C:173 , THR C:174 , ILE C:200 , PRO C:202 , SER C:206 , THR C:207 , ARG C:230 , CL C:403 , HOH C:505 , HOH C:523 , HOH C:527 , HOH C:538 , HOH C:577binding site for residue A2R C 404
12AD3SOFTWAREASN D:13 , ARG D:286 , HOH D:638binding site for residue CL D 401
13AD4SOFTWAREARG D:230 , HIS D:277 , A2R D:403 , HOH D:551binding site for residue CL D 402
14AD5SOFTWAREVAL D:72 , GLY D:73 , PHE D:148 , LEU D:150 , GLY D:151 , ARG D:152 , ILE D:153 , THR D:172 , ARG D:173 , THR D:174 , ILE D:200 , VAL D:201 , PRO D:202 , SER D:206 , THR D:207 , VAL D:228 , GLY D:229 , ARG D:230 , CL D:402 , HOH D:506 , HOH D:507 , HOH D:517 , HOH D:539 , HOH D:547 , HOH D:564 , HOH D:569binding site for residue A2R D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J23)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:259 -Pro A:260
2Glu B:259 -Pro B:260
3Glu C:259 -Pro C:260
4Glu D:259 -Pro D:260

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J23)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J23)

(-) Exons   (0, 0)

(no "Exon" information available for 5J23)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh...eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhhh..eeeee..........ee..hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j23 A   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRAI 320
                                    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        


Chain B from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh...eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhh...eeeee..........ee..hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j23 B   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRAI 320
                                    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        


Chain C from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh...eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhhh..eeeee..........ee..hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j23 C   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRAI 320
                                    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        


Chain D from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh...eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhh...eeeee..........ee..hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j23 D   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRAI 320
                                    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
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5J23)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J23)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J23)

(-) Gene Ontology  (4, 4)

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  5j23
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        Q92LZ4_RHIME | Q92LZ4: 5uog 5v6q 5v72 5v7g 5v7n

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