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(-) Description

Title :  CRYSTAL STRUCTURE OF LACTALDEHYDE REDUCTASE
 
Authors :  D. Kumaran, S. Swaminathan, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  08 Dec 03  (Deposition) - 17 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Dehydrogenase, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Kumaran, S. Swaminathan
Crystal Structure Of Lactaldehyde Reductase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACTALDEHYDE REDUCTASE
    ChainsA, B
    EC Number1.1.1.77
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneFUCO, B2799, Z4116, ECS3659
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPROPANEDIOL OXIDOREDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 32)

Asymmetric/Biological Unit (5, 32)
No.NameCountTypeFull Name
1APR2Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
2FE22Ligand/IonFE (II) ION
3MSE24Mod. Amino AcidSELENOMETHIONINE
4PGO2Ligand/IonS-1,2-PROPANEDIOL
5ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:196 , HIS A:200 , HIS A:263 , HIS A:277 , PGO A:390 , HOH A:713BINDING SITE FOR RESIDUE ZN A 387
2AC2SOFTWAREASP B:196 , HIS B:200 , HIS B:263 , HIS B:277 , PGO B:390 , HOH B:532BINDING SITE FOR RESIDUE ZN B 387
3AC3SOFTWARECYS A:362BINDING SITE FOR RESIDUE FE2 A 388
4AC4SOFTWARECYS B:362BINDING SITE FOR RESIDUE FE2 B 388
5AC5SOFTWAREASP A:39 , THR A:41 , LEU A:42 , PRO A:70 , ASN A:71 , GLY A:97 , GLY A:98 , SER A:99 , PRO A:100 , THR A:140 , THR A:141 , THR A:144 , VAL A:153 , LYS A:162 , MSE A:181 , GLY A:184 , MSE A:185 , LEU A:189 , THR A:193 , HIS A:277 , PGO A:390 , HOH A:415 , HOH A:428 , HOH A:429 , HOH A:441 , HOH A:447 , HOH A:459 , HOH A:468 , HOH A:636 , HOH A:675 , HOH A:713BINDING SITE FOR RESIDUE APR A 389
6AC6SOFTWAREASP B:39 , THR B:41 , LEU B:42 , PRO B:70 , ASN B:71 , PRO B:72 , GLY B:97 , GLY B:98 , SER B:99 , PRO B:100 , THR B:140 , THR B:141 , THR B:144 , VAL B:153 , LYS B:162 , MSE B:181 , GLY B:184 , MSE B:185 , LEU B:189 , THR B:193 , HIS B:277 , PGO B:390 , HOH B:400 , HOH B:415 , HOH B:428 , HOH B:459 , HOH B:472 , HOH B:474 , HOH B:488 , HOH B:532 , HOH B:651 , HOH B:666 , HOH B:688BINDING SITE FOR RESIDUE APR B 389
7AC7SOFTWAREASN A:151 , HIS A:200 , PHE A:254 , HIS A:263 , HIS A:277 , ZN A:387 , APR A:389 , HOH A:402 , HOH A:415 , HOH A:713BINDING SITE FOR RESIDUE PGO A 390
8AC8SOFTWAREASN B:151 , HIS B:200 , PHE B:254 , HIS B:263 , HIS B:277 , ZN B:387 , APR B:389 , HOH B:415 , HOH B:472 , HOH B:532BINDING SITE FOR RESIDUE PGO B 390

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RRM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RRM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RRM)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_IRON_1PS00913 Iron-containing alcohol dehydrogenases signature 1.FUCO_ECOLI174-202
 
  2A:175-203
B:175-203
2ADH_IRON_2PS00060 Iron-containing alcohol dehydrogenases signature 2.FUCO_ECOLI259-279
 
  2A:260-280
B:260-280

(-) Exons   (0, 0)

(no "Exon" information available for 1RRM)

(-) 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:385
 aligned with FUCO_ECOLI | P0A9S1 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:385
                                                                                                                                                                                                                                                                                                                                                                                                                       382   
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380 |   
           FUCO_ECOLI     1 MANRMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAGEEMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVMGVKVEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVCTGGNPREATLEDIVELYHTAW---   -
               SCOP domains d1rrma_ A: Lactaldehyde reductase FucO                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -1rrmA01 A:3-186  [code=3.40.50.1970, no name defined]                                                                                                                                   1rrmA02 A:187-386 Dehydroquinate synthase-like - alpha domain                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee..hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh.hhhhhee.........eeeee...........eeeeee....eeeeee.hhhh..eeeehhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_IRON_1  PDB: A:175-203   --------------------------------------------------------ADH_IRON_2           ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rrm A   2 mANRmILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKmDAAGLAWAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADmmDGmPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAGEEmALGQYVAGmGFSNVGLGLVHGmAHPLGAFYNTPHGVANAILLPHVmRYNADFTGEKYRDIARVmGVKVEGmSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVCTGGNPREATLEDIVELYHTAWEGG 386
                            |   |   11        21        31        41        51   |    61        71        81        91       101       111       121       131       141       151       161       171       181|  |   191       201       211       221       231       241 |     251|      261   |   271       281       291       301     | 311  |    321       331       341       351       361       371       381     
                            |   |                                               55-MSE                                                                                                                       181-MSE                                                       243-MSE  252-MSE      265-MSE                 289-MSE           307-MSE  |                                                                        
                            2-MSE                                                                                                                                                                             182-MSE                                                                                                                             314-MSE                                                                    
                                6-MSE                                                                                                                                                                            185-MSE                                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:384
 aligned with FUCO_ECOLI | P0A9S1 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:384
                                                                                                                                                                                                                                                                                                                                                                                                                       382  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380 |  
           FUCO_ECOLI     1 MANRMILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAGEEMALGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVMGVKVEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVCTGGNPREATLEDIVELYHTAW--   -
               SCOP domains d1rrmb_ B: Lactaldehyde reductase FucO                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -1rrmB01 B:3-186  [code=3.40.50.1970, no name defined]                                                                                                                                   1rrmB02 B:187-385 Dehydroquinate synthase-like - alpha domain                                                                                                                                           CATH domains
           Pfam domains (1) --------Fe-ADH-1rrmB01 B:10-376                                                                                                                                                                                                                                                                                                                                                        --------- Pfam domains (1)
           Pfam domains (2) --------Fe-ADH-1rrmB02 B:10-376                                                                                                                                                                                                                                                                                                                                                        --------- Pfam domains (2)
         Sec.struct. author ..eeee...eeee..hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh.hhhhhee.........eeeee...........eeeeee....eeeeee.hhhh..eeeehhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_IRON_1  PDB: B:175-203   --------------------------------------------------------ADH_IRON_2           --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rrm B   2 mANRmILNETAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKmDAAGLAWAIYDGVVPNPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSVPILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADmmDGmPPALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKDAGEEmALGQYVAGmGFSNVGLGLVHGmAHPLGAFYNTPHGVANAILLPHVmRYNADFTGEKYRDIARVmGVKVEGmSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVCTGGNPREATLEDIVELYHTAWEG 385
                            |   |   11        21        31        41        51   |    61        71        81        91       101       111       121       131       141       151       161       171       181|  |   191       201       211       221       231       241 |     251|      261   |   271       281       291       301     | 311  |    321       331       341       351       361       371       381    
                            2-MSE                                               55-MSE                                                                                                                       181-MSE                                                       243-MSE  252-MSE      265-MSE                 289-MSE           307-MSE  |                                                                       
                                6-MSE                                                                                                                                                                         182-MSE                                                                                                                             314-MSE                                                                   
                                                                                                                                                                                                                 185-MSE                                                                                                                                                                                                    

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: DHQS (27)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FUCO_ECOLI | P0A9S1)
molecular function
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0008912    lactaldehyde reductase activity    Catalysis of the reaction: propane-1,2-diol + NAD+ = lactaldehyde + NADH + H+.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0042355    L-fucose catabolic process    The chemical reactions and pathways resulting in the breakdown of L-fucose (6-deoxy-Lgalactose).
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019317    fucose catabolic process    The chemical reactions and pathways resulting in the breakdown of fucose (6-deoxygalactose).
    GO:0006004    fucose metabolic process    The chemical reactions and pathways involving fucose, or 6-deoxygalactose, which has two enantiomers, D-fucose and L-fucose.
    GO:0042846    glycol catabolic process    The chemical reactions and pathways resulting in the breakdown of glycol, a diol in which the two hydroxy groups are on different carbon atoms, usually but not necessarily adjacent.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0051143    propanediol metabolic process    The chemical reactions and pathways involving propanediol, CH3-CHOH-CH2OH, a sweet, colorless, viscous, hygroscopic liquid used as an antifreeze, in brake fluid and as a humectant in cosmetics and personal care items.
    GO:0019301    rhamnose catabolic process    The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FUCO_ECOLI | P0A9S12bi4 2bl4 5br4

(-) Related Entries Specified in the PDB File

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