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(-) Description

Title :  CRYSTAL STRUCTURE OF S-2-HYDROXYPROPYL COENZYME M DEHYDROGENASE (S-HPCDH) BOUND TO S-HPC AND NADH
 
Authors :  J. W. Bakelar, S. J. Johnson
Date :  18 Jan 13  (Deposition) - 27 Mar 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Bakelar, D. A. Sliwa, S. J. Johnson
Crystal Structures Of S-Hpcdh Reveal Determinants Of Stereospecificity For R- And S-Hydroxypropyl-Coenzyme M Dehydrogenases.
Arch. Biochem. Biophys. V. 533 62 2013
PubMed-ID: 23474457  |  Reference-DOI: 10.1016/J.ABB.2013.02.017

(-) Compounds

Molecule 1 - SHORT-CHAIN DEHYDROGENASE/REDUCTASE SDR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: XANTHOBACTER AUTOTROPHICUS
    Organism Taxid: 78245
    Strain: PY2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
11HS4Ligand/Ion2-{[(2S)-2-HYDROXYPROPYL]SULFANYL}ETHANESULFONIC ACID
2NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , GLY A:18 , ILE A:19 , ASP A:38 , LEU A:39 , ALA A:63 , ASP A:64 , VAL A:65 , ASN A:91 , GLY A:93 , ARG A:110 , VAL A:114 , PHE A:141 , GLY A:142 , SER A:143 , TYR A:156 , LYS A:160 , PRO A:186 , GLY A:187 , THR A:188 , VAL A:189 , THR A:192 , GLY A:193 , MET A:194 , 1HS A:302 , HOH A:404 , HOH A:413 , HOH A:421 , HOH A:445 , HOH A:463 , HOH A:518 , HOH A:577BINDING SITE FOR RESIDUE NAI A 301
2AC2SOFTWARESER A:143 , TYR A:156 , THR A:188 , ARG A:211 , TYR A:215 , MET A:252 , NAI A:301BINDING SITE FOR RESIDUE 1HS A 302
3AC3SOFTWAREGLY B:14 , GLY B:18 , ILE B:19 , ASP B:38 , LEU B:39 , ALA B:63 , ASP B:64 , VAL B:65 , ASN B:91 , GLY B:93 , ARG B:110 , VAL B:114 , PHE B:141 , GLY B:142 , SER B:143 , TYR B:156 , LYS B:160 , PRO B:186 , GLY B:187 , THR B:188 , VAL B:189 , THR B:192 , GLY B:193 , MET B:194 , 1HS B:302 , HOH B:440 , HOH B:454 , HOH B:470 , HOH B:471 , HOH B:480 , HOH B:510BINDING SITE FOR RESIDUE NAI B 301
4AC4SOFTWARESER B:143 , TYR B:156 , THR B:188 , LEU B:198 , ARG B:211 , TYR B:215 , MET B:252 , NAI B:301 , HOH B:545BINDING SITE FOR RESIDUE 1HS B 302
5AC5SOFTWAREGLY C:14 , GLY C:18 , ILE C:19 , ASP C:38 , LEU C:39 , ALA C:63 , ASP C:64 , VAL C:65 , ASN C:91 , GLY C:93 , ARG C:110 , PHE C:141 , GLY C:142 , SER C:143 , TYR C:156 , LYS C:160 , PRO C:186 , GLY C:187 , THR C:188 , VAL C:189 , THR C:192 , GLY C:193 , MET C:194 , 1HS C:302 , HOH C:404 , HOH C:421 , HOH C:427 , HOH C:443 , HOH C:470 , HOH C:483 , HOH C:558 , HOH C:570BINDING SITE FOR RESIDUE NAI C 301
6AC6SOFTWARESER C:143 , VAL C:144 , TYR C:156 , THR C:188 , LEU C:198 , ARG C:211 , TYR C:215 , MET C:252 , NAI C:301 , HOH C:523 , HOH C:569BINDING SITE FOR RESIDUE 1HS C 302
7AC7SOFTWAREGLY D:14 , GLY D:18 , ILE D:19 , ASP D:38 , LEU D:39 , ALA D:63 , ASP D:64 , VAL D:65 , ASN D:91 , GLY D:93 , VAL D:114 , PHE D:141 , GLY D:142 , SER D:143 , TYR D:156 , LYS D:160 , PRO D:186 , GLY D:187 , THR D:188 , VAL D:189 , THR D:192 , GLY D:193 , MET D:194 , 1HS D:302 , HOH D:426 , HOH D:436 , HOH D:458 , HOH D:469 , HOH D:475 , HOH D:487 , HOH D:490 , HOH D:583BINDING SITE FOR RESIDUE NAI D 301
8AC8SOFTWARESER D:143 , TYR D:156 , THR D:188 , ARG D:211 , TYR D:215 , MET D:252 , NAI D:301 , HOH D:449BINDING SITE FOR RESIDUE 1HS D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn D:3 -Arg D:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ITU)

(-) Sequences/Alignments

Asymmetric/Biological 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:253
                                                                                                                                                                                                                                                                                             
               SCOP domains d4itua_ A: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4itu A   3 NRLKNEVIAITGGGAGIGLAIASAALREGAKVALIDLDQGLAERSAAMLSTGGAVAKGFGADVTKAADITAAITSAEQTIGSLTGLVNNAGIAGFGSVHDADAAAWDRIMAVNVTGTFLASKAALAGMLERHKGTIVNFGSVAGLVGIPTMAAYCAAKGAIVNLTRQMAADYSGRGVRVNAVCPGTVTSTGMGQQLLGSDTSPEVQARRLAKYPIGRFGTPEDIAEAVIFLLSDQAAFVTGAAFAVDGGMTAI 255
                                    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   


Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains d4itub_ B: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhh.hhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4itu B   3 NRLKNEVIAITGGGAGIGLAIASAALREGAKVALIDLDQGLAERSAAMLSTGGAVAKGFGADVTKAADITAAITSAEQTIGSLTGLVNNAGIAGFGSVHDADAAAWDRIMAVNVTGTFLASKAALAGMLERHKGTIVNFGSVAGLVGIPTMAAYCAAKGAIVNLTRQMAADYSGRGVRVNAVCPGTVTSTGMGQQLLGSPEVQARRLAKYPIGRFGTPEDIAEAVIFLLSDQAAFVTGAAFAVDGGMTAI 255
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       205       215       225       235       245       255
                                                                                                                                                                                                                               200|                                                   
                                                                                                                                                                                                                                204                                                   


Chain C from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains d4ituc_ C: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4itu C   3 NRLKNEVIAITGGGAGIGLAIASAALREGAKVALIDLDQGLAERSAAMLSTGGAVAKGFGADVTKAADITAAITSAEQTIGSLTGLVNNAGIAGFGSVHDADAAAWDRIMAVNVTGTFLASKAALAGMLERHKGTIVNFGSVAGLVGIPTMAAYCAAKGAIVNLTRQMAADYSGRGVRVNAVCPGTVTSTGMGQQLLVQARRLAKYPIGRFGTPEDIAEAVIFLLSDQAAFVTGAAFAVDGGMTAI 255
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192      |209       219       229       239       249      
                                                                                                                                                                                                                              199|                                                
                                                                                                                                                                                                                               207                                                


Chain D from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains d4itud_ D: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhh.hhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4itu D   3 NRLKNEVIAITGGGAGIGLAIASAALREGAKVALIDLDQGLAERSAAMLSTGGAVAKGFGADVTKAADITAAITSAEQTIGSLTGLVNNAGIAGFGSVHDADAAAWDRIMAVNVTGTFLASKAALAGMLERHKGTIVNFGSVAGLVGIPTMAAYCAAKGAIVNLTRQMAADYSGRGVRVNAVCPGTVTSTGMGQQLLGPEVQARRLAKYPIGRFGTPEDIAEAVIFLLSDQAAFVTGAAFAVDGGMTAI 255
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       206       216       226       236       246         
                                                                                                                                                                                                                               200|                                                  
                                                                                                                                                                                                                                205
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A7IQH5_XANP2 | A7IQH5: 4gh5

(-) Related Entries Specified in the PDB File

4gh5 THE SAME PROTEIN BOUND TO NAD+