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(-) Description

Title :  CRYSTAL STRUCTURE OF ALCOHOL DEHYDROGENASE, IRON-CONTAINING (TM0920) FROM THERMOTOGA MARITIMA AT 1.30 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  27 Feb 03  (Deposition) - 10 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tm0920, Alcohol Dehydrogenase, Iron-Containing, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Schwarzenbacher, F. Von Delft, J. M. Canaves, L. S. Brinen, X. Dai, A. M. Deacon, M. A. Elsliger, S. Eshaghi, R. Floyd, A. Godzik, C. Grittini, S. K. Grzechnik, C. Guda, L. Jaroszewski, C. Karlak, H. E. Klock, E. Koesema, J. S. Kovarik, A. Kreusch, P. Kuhn, S. A. Lesley, D. Mcmullan, T. M. Mcphillips, M. A. Miller, M. D. Miller, A. Morse, K. Moy, J. Ouyang, R. Page, A. Robb, K. Rodrigues, T. L. Selby, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, X. Wang, B. West, G. Wolf, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of An Iron-Containing 1, 3-Propanediol Dehydrogenase (Tm0920) From Thermotoga Maritima At 1. 3 A Resolution
Proteins V. 54 174 2004
PubMed-ID: 14705036  |  Reference-DOI: 10.1002/PROT.10594
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALCOHOL DEHYDROGENASE, IRON-CONTAINING
    Chains: A, B
    EC Number: 1.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0920
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 28)

Asymmetric Unit (4, 28)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2MSE22Mod. Amino AcidSELENOMETHIONINE
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MSE11Mod. Amino AcidSELENOMETHIONINE
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MSE11Mod. Amino AcidSELENOMETHIONINE
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:189 , HIS A:193 , HIS A:256 , HIS A:270 , NAP A:1800BINDING SITE FOR RESIDUE FE A 900
2AC2SOFTWAREASP B:189 , HIS B:193 , HIS B:256 , HIS B:270 , NAP B:1801BINDING SITE FOR RESIDUE FE B 900
3AC3SOFTWAREGLY A:36 , SER A:38 , SER A:39 , ASN A:43 , GLU A:68 , ASN A:69 , GLY A:95 , GLY A:96 , SER A:97 , PRO A:98 , ASP A:100 , THR A:136 , THR A:137 , THR A:140 , SER A:142 , THR A:145 , TYR A:147 , ILE A:149 , LYS A:157 , TYR A:174 , SER A:177 , MSE A:178 , LEU A:182 , THR A:186 , ASP A:189 , HIS A:193 , HIS A:270 , FE A:900 , HOH A:2827 , HOH A:2833 , HOH A:2842 , HOH A:2843 , HOH A:2850 , HOH A:2852 , HOH A:2884 , HOH A:2982 , HOH A:2983 , HOH A:3020 , HOH A:3125 , HOH A:3133 , HOH A:3190 , HOH A:3213BINDING SITE FOR RESIDUE NAP A 1800
4AC4SOFTWAREGLY B:36 , SER B:38 , SER B:39 , ASN B:43 , GLU B:68 , ASN B:69 , GLY B:95 , GLY B:96 , SER B:97 , PRO B:98 , ASP B:100 , THR B:136 , THR B:137 , THR B:140 , SER B:142 , THR B:145 , TYR B:147 , ILE B:149 , LYS B:157 , TYR B:174 , SER B:177 , MSE B:178 , LEU B:182 , THR B:186 , HIS B:193 , HIS B:270 , FE B:900 , HOH B:2821 , HOH B:2822 , HOH B:2824 , HOH B:2837 , HOH B:2876 , HOH B:2879 , HOH B:2951 , HOH B:2980 , HOH B:2985 , HOH B:2988 , HOH B:3047 , HOH B:3085 , HOH B:3153 , HOH B:3200 , HOH B:3208BINDING SITE FOR RESIDUE NAP B 1801
5AC5SOFTWAREGLU B:3 , TYR B:5 , HOH B:2948 , HOH B:2956 , HOH B:3021 , HOH B:3081 , HOH B:3105 , HOH B:3202BINDING SITE FOR RESIDUE TRS B 2800
6AC6SOFTWAREGLU A:55 , THR A:56 , GLU A:57 , HOH A:3025 , HOH A:3067 , LYS B:41 , LYS B:42 , ASN B:43 , GLY B:44 , HOH B:2920 , HOH B:3046 , HOH B:3100BINDING SITE FOR RESIDUE TRS A 2801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O2D)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:138 -Gly A:139
2Ala B:138 -Gly B:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O2D)

(-) Exons   (0, 0)

(no "Exon" information available for 1O2D)

(-) 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:359
 aligned with Q9X022_THEMA | Q9X022 from UniProtKB/TrEMBL  Length:359

    Alignment length:359
                                    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         
         Q9X022_THEMA     1 MWEFYMPTDVFFGEKILEKRGNIIDLLGKRALVVTGKSSSKKNGSLDDLKKLLDETEISYEIFDEVEENPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFAKAVAVLLKEKDLSVEDLYDREKVKHWLPVVEIPTTAGTGSEVTPYSILTDPEGNKRGCTLMFPVYAFLDPRYTYSMSDELTLSTGVDALSHAVEGYLSRKSTPPSDALAIEAMKIIHRNLPKAIEGNREARKKMFVASCLAGMVIAQTGTTLAHALGYPLTTEKGIKHGKATGMVLPFVMEVMKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVSSEELEKWVEKGSRAKHLKNTPGTFTPEKIRNIYREALGV 359
               SCOP domains d1o2da_ A: Alcohol dehydrogenase TM0920                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------1o2dA01 A:7-179  [code=3.40.50.1970, no name defined]                                                                                                                        1o2dA02 A:180-358 Dehydroquinate synthase-like - alpha domain                                                                                                                      - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..hhhhhhhhhhhhh..eeeeeee.hhhhh.hhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh......hhhhhhhhhh.....eeeee.....hhhhh.eeeee.....eeeee.....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o2d A   1 VWEFYmPTDVFFGEKILEKRGNIIDLLGKRALVVTGKSSSKKNGSLDDLKKLLDETEISYEIFDEVEENPSFDNVmKAVERYRNDSFDFVVGLGGGSPmDFAKAVAVLLKEKDLSVEDLYDREKVKHWLPVVEIPTTAGTGSEVTPYSILTDPEGNKRGCTLmFPVYAFLDPRYTYSmSDELTLSTGVDALSHAVEGYLSRKSTPPSDALAIEAmKIIHRNLPKAIEGNREARKKmFVASCLAGmVIAQTGTTLAHALGYPLTTEKGIKHGKATGmVLPFVmEVmKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVSSEELEKWVEKGSRAKHLKNTPGTFTPEKIRNIYREALGV 359
                                 |  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         
                                 6-MSE                                                                76-MSE                 99-MSE                                                         163-MSE        178-MSE                              215-MSE              236-MSE  245-MSE                        276-MSE |  |                                                                          
                                                                                                                                                                                                                                                                                                                   282-MSE                                                                         
                                                                                                                                                                                                                                                                                                                      285-MSE                                                                      


Chain B from PDB  Type:PROTEIN  Length:360
 aligned with Q9X022_THEMA | Q9X022 from UniProtKB/TrEMBL  Length:359

    Alignment length:360
                              1                                                                                                                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358
         Q9X022_THEMA     - --MWEFYMPTDVFFGEKILEKRGNIIDLLGKRALVVTGKSSSKKNGSLDDLKKLLDETEISYEIFDEVEENPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFAKAVAVLLKEKDLSVEDLYDREKVKHWLPVVEIPTTAGTGSEVTPYSILTDPEGNKRGCTLMFPVYAFLDPRYTYSMSDELTLSTGVDALSHAVEGYLSRKSTPPSDALAIEAMKIIHRNLPKAIEGNREARKKMFVASCLAGMVIAQTGTTLAHALGYPLTTEKGIKHGKATGMVLPFVMEVMKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVSSEELEKWVEKGSRAKHLKNTPGTFTPEKIRNIYREALG 358
               SCOP domains d1o2db_ B: Alcohol dehydrogenase TM0920                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------1o2dB01 B:7-179  [code=3.40.50.1970, no name defined]                                                                                                                        1o2dB02 B:180-358 Dehydroquinate synthase-like - alpha domain                                                                                                                       CATH domains
           Pfam domains (1) --------Fe-ADH-1o2dB01 B:7-349                                                                                                                                                                                                                                                                                                                                 --------- Pfam domains (1)
           Pfam domains (2) --------Fe-ADH-1o2dB02 B:7-349                                                                                                                                                                                                                                                                                                                                 --------- Pfam domains (2)
         Sec.struct. author ..........eeee..hhhhhhhhhhhhhh.eeeeeee.hhhhh.hhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhh....hhhhhh.........eeeee.....hhhhh.eeeee.....eeeee.....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o2d B  -1 HHVWEFYmPTDVFFGEKILEKRGNIIDLLGKRALVVTGKSSSKKNGSLDDLKKLLDETEISYEIFDEVEENPSFDNVmKAVERYRNDSFDFVVGLGGGSPmDFAKAVAVLLKEKDLSVEDLYDREKVKHWLPVVEIPTTAGTGSEVTPYSILTDPEGNKRGCTLmFPVYAFLDPRYTYSmSDELTLSTGVDALSHAVEGYLSRKSTPPSDALAIEAmKIIHRNLPKAIEGNREARKKmFVASCLAGmVIAQTGTTLAHALGYPLTTEKGIKHGKATGmVLPFVmEVmKEEIPEKVDTVNHIFGGSLLKFLKELGLYEKVAVSSEELEKWVEKGSRAKHLKNTPGTFTPEKIRNIYREALG 358
                                   | 8        18        28        38        48        58        68       |78        88        98|      108       118       128       138       148       158    |  168       178       188       198       208      |218       228       238      |248       258       268       278   |  |288       298       308       318       328       338       348       358
                                   6-MSE                                                                76-MSE                 99-MSE                                                         163-MSE        178-MSE                              215-MSE              236-MSE  245-MSE                        276-MSE |  |                                                                         
                                                                                                                                                                                                                                                                                                                     282-MSE                                                                        
                                                                                                                                                                                                                                                                                                                        285-MSE
   Legend:   → Mismatch (orange background)
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    → 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 Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: DHQS (27)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9X022_THEMA | Q9X022)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9X022_THEMA | Q9X022: 1vhd

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