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(-) Description

Title :  UNDA COMPLEXED WITH 2,3-DODECENOIC ACID
 
Authors :  X. Li, J. D. H. Cate
Date :  13 Nov 14  (Deposition) - 24 Dec 14  (Release) - 07 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Non-Heme Iron Dependent Desaturase/Decarboxylase, 1-Undecene Biosynthesis, Aliphatic Medium-Chain 1-Alkene Biosynthesis, Metalloenzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Rui, X. Li, X. Zhu, J. Liu, B. Domigan, I. Barr, J. H. Cate, W. Zhang
Microbial Biosynthesis Of Medium-Chain 1-Alkenes By A Nonheme Iron Oxidase.
Proc. Natl. Acad. Sci. Usa V. 111 18237 2014
PubMed-ID: 25489112  |  Reference-DOI: 10.1073/PNAS.1419701112

(-) Compounds

Molecule 1 - TENA/THI-4 FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PFL_4321
    Organism Scientific: PSEUDOMONAS PROTEGENS PF-5
    Organism Taxid: 220664
    Synonym: UNDA, OXYGEN-ACTIVATING NON-HEME IRON DEPENDENT DESATURASE/DECARBOXYLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
13X12Ligand/Ion(2E)-DODEC-2-ENOIC ACID
2FE2Ligand/IonFE (III) ION
3OXY1Ligand/IonOXYGEN MOLECULE
4PSL2Ligand/IonPYROSULFATE
5SO48Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
13X12Ligand/Ion(2E)-DODEC-2-ENOIC ACID
2FE-1Ligand/IonFE (III) ION
3OXY-1Ligand/IonOXYGEN MOLECULE
4PSL2Ligand/IonPYROSULFATE
5SO48Ligand/IonSULFATE ION
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
13X12Ligand/Ion(2E)-DODEC-2-ENOIC ACID
2FE-1Ligand/IonFE (III) ION
3OXY2Ligand/IonOXYGEN MOLECULE
4PSL2Ligand/IonPYROSULFATE
5SO48Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:101 , HIS A:104 , HIS A:194 , 3X1 A:302 , HOH A:478binding site for residue FE A 301
02AC2SOFTWARETYR A:41 , TYR A:57 , GLU A:101 , HIS A:104 , GLU A:159 , THR A:162 , TRP A:190 , HIS A:194 , FE A:301 , HOH A:478 , HOH A:534binding site for residue 3X1 A 302
03AC3SOFTWAREARG A:99 , ASN A:103 , HIS A:104 , TYR A:107 , HOH A:485 , HOH A:531 , HOH A:604binding site for residue PSL A 303
04AC4SOFTWAREARG A:92 , ARG A:96 , HOH A:520 , HOH A:585binding site for residue SO4 A 304
05AC5SOFTWAREARG A:113 , THR A:118 , LEU A:119 , HOH A:527 , HOH A:552 , HOH A:617 , HOH A:644binding site for residue SO4 A 305
06AC6SOFTWARETHR A:218 , LYS A:219 , ALA A:220 , HOH A:638binding site for residue SO4 A 306
07AC7SOFTWAREARG A:96 , ARG A:99binding site for residue SO4 A 307
08AC8SOFTWAREGLU B:101 , HIS B:104 , HIS B:194 , 3X1 B:302 , OXY B:303binding site for residue FE B 301
09AC9SOFTWARETYR B:41 , TYR B:57 , GLU B:101 , HIS B:104 , GLU B:159 , TRP B:190 , HIS B:194 , FE B:301 , OXY B:303 , HOH B:450binding site for residue 3X1 B 302
10AD1SOFTWAREGLU B:101 , HIS B:104 , GLU B:159 , HIS B:194 , FE B:301 , 3X1 B:302binding site for residue OXY B 303
11AD2SOFTWAREARG B:99 , ASN B:103 , HIS B:104 , TYR B:107 , LYS B:189 , HOH B:429binding site for residue PSL B 304
12AD3SOFTWAREARG B:92 , ARG B:96 , HOH B:520binding site for residue SO4 B 305
13AD4SOFTWARETHR B:218 , LYS B:219 , HOH B:534binding site for residue SO4 B 306
14AD5SOFTWAREARG B:113 , THR B:118 , LEU B:119 , HOH B:442 , HOH B:509binding site for residue SO4 B 307
15AD6SOFTWAREARG B:43 , LYS B:48binding site for residue SO4 B 308

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WWZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WWZ)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wwz A   2 IDTFSRTGPLMEAASYPAWTQQLIQDCSESKRRVVEHELYQRMRDNKLSAKVMRQYLIGGWPVVEQFALYMAQNLTKTRFARHPGEDMARRWLMRNIRVELNHADYWVHWSRAHGVTLEDLQAQQVPPELHALSHWCWHTSSADSLIVAIAATNYAIEGATGEWSALVCSNGIYAAAFPEEDRKRAMKWLKMHAQYDDAHPWEALEIIVTLAGLNPTKALQAELRQAICKSYDYMYLFLERCMQQEKTAVTRERLA 257
                                    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      


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wwz B   2 IDTFSRTGPLMEAASYPAWTQQLIQDCSESKRRVVEHELYQRMRDNKLSAKVMRQYLIGGWPVVEQFALYMAQNLTKTRFARHPGEDMARRWLMRNIRVELNHADYWVHWSRAHGVTLEDLQAQQVPPELHALSHWCWHTSSADSLIVAIAATNYAIEGATGEWSALVCSNGIYAAAFPEEDRKRAMKWLKMHAQYDDAHPWEALEIIVTLAGLNPTKALQAELRQAICKSYDYMYLFLERCMQQEKTAVTRERLA 257
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 4WWZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        Q4K8M0_PSEF5 | Q4K8M0: 4wwj 4wx0

(-) Related Entries Specified in the PDB File

4wwj STRUCTURE OF UNDA
4wx0 UNDA COMPLEXED WITH BETA-HYDROXYDODECANOIC ACID