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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE LACCASE (YFIH) FROM ESCHERICHIA COLI AT 1.54 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  04 Apr 05  (Deposition) - 12 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative Laccase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Upf0124 Protein Yfih (Np_417084. 1) From Escherichia Coli K12 At 1. 54 A Resolutio
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL UPF0124 PROTEIN YFIH
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YFIH
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2EDO19Ligand/Ion1,2-ETHANEDIOL
3MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:115 , GLU A:163 , VAL A:164 , GLY A:165 , LYS A:189 , ARG A:228 , EDO A:248 , EDO A:264BINDING SITE FOR RESIDUE CIT A 244
02AC2SOFTWAREHIS A:71 , THR A:104 , ALA A:105 , ASP A:106 , CYS A:107 , HIS A:124 , TYR A:227 , ARG A:235 , HOH A:281 , HOH A:426 , HOH A:470BINDING SITE FOR RESIDUE CIT A 245
03AC3SOFTWARELEU A:28 , ASN A:43 , HIS A:46 , VAL A:205 , HOH A:278 , HOH A:348BINDING SITE FOR RESIDUE EDO A 246
04AC4SOFTWAREARG A:22 , ILE A:23 , GLY A:24 , ASP A:32 , SER A:33 , GLU A:222 , EDO A:253BINDING SITE FOR RESIDUE EDO A 247
05AC5SOFTWAREPRO A:10 , PRO A:12 , ARG A:115 , LYS A:189 , CIT A:244BINDING SITE FOR RESIDUE EDO A 248
06AC6SOFTWAREPRO A:159 , ALA A:181 , ALA A:182 , ILE A:184 , LEU A:191 , GLN A:196BINDING SITE FOR RESIDUE EDO A 249
07AC7SOFTWAREGLY A:58 , HOH A:459BINDING SITE FOR RESIDUE EDO A 250
08AC8SOFTWARELEU A:67 , GLN A:69 , EDO A:257 , HOH A:412BINDING SITE FOR RESIDUE EDO A 251
09AC9SOFTWAREASP A:106 , CYS A:107 , LEU A:108 , ALA A:125 , GLY A:126 , TRP A:127 , PHE A:162 , ILE A:194 , HOH A:407BINDING SITE FOR RESIDUE EDO A 252
10BC1SOFTWAREASP A:32 , ASN A:221 , EDO A:247 , HOH A:333BINDING SITE FOR RESIDUE EDO A 253
11BC2SOFTWAREASP A:193 , TYR A:195 , ARG A:199 , GLY A:213 , EDO A:258 , EDO A:263BINDING SITE FOR RESIDUE EDO A 254
12BC3SOFTWAREVAL A:139 , PHE A:142 , ASP A:144 , PRO A:146 , HOH A:289 , HOH A:404BINDING SITE FOR RESIDUE EDO A 255
13BC4SOFTWAREARG A:128BINDING SITE FOR RESIDUE EDO A 256
14BC5SOFTWAREARG A:51 , EDO A:251 , HOH A:279BINDING SITE FOR RESIDUE EDO A 257
15BC6SOFTWAREPRO A:159 , GLY A:213 , ARG A:215 , EDO A:254BINDING SITE FOR RESIDUE EDO A 258
16BC7SOFTWARETYR A:218 , THR A:219 , ASN A:221 , ARG A:229 , HOH A:305 , HOH A:309BINDING SITE FOR RESIDUE EDO A 259
17BC8SOFTWAREPRO A:44 , ARG A:51 , HOH A:334BINDING SITE FOR RESIDUE EDO A 260
18BC9SOFTWAREGLU A:48 , LYS A:52 , HOH A:443 , HOH A:454BINDING SITE FOR RESIDUE EDO A 261
19CC1SOFTWAREPHE A:55 , LEU A:60 , SER A:62 , HOH A:445BINDING SITE FOR RESIDUE EDO A 262
20CC2SOFTWAREGLY A:212 , GLY A:213 , EDO A:254BINDING SITE FOR RESIDUE EDO A 263
21CC3SOFTWARETRP A:127 , PHE A:162 , ARG A:228 , CIT A:244 , HOH A:389 , HOH A:398BINDING SITE FOR RESIDUE EDO A 264

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z9T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:29 -Pro A:30
2Asp A:32 -Ser A:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z9T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z9T)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z9T)

(-) 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:240
 aligned with YFIH_ECOLI | P33644 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
           YFIH_ECOLI     2 SKLIVPQWPQPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVMTADCLPVLFCNRAGTEVAAAHAGWRGLCAGVLEETVSCFADNPENILAWLGPAIGPRAFEVGGEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLI 243
               SCOP domains d1z9ta_ A: Hypothetical protein yfiH                                                                                                                                                                                                               SCOP domains
               CATH domains 1z9tA00 A:2-243 CNF1/YfiH-like putative cysteine hydrolases                                                                                                                                                                                        CATH domains
               Pfam domains -----------------Cu-oxidase_4-1z9tA01 A:19-242                                                                                                                                                                                                   - Pfam domains
         Sec.struct. author ..ee.........eeeeee......................hhhhhhhhhhhhhhhh................eee...--.......eeee.....eeeeee...eeeeeee.....eeeeeehhhhhhhhhhhhhhhh...hhh.eeeee.........eehhhhhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhhhh...eeee.............hhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9t A   2 SKLIVPQWPQPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTG--YASKRADASYSNTPGTVCAVmTADCLPVLFCNRAGTEVAAAHAGWRGLCAGVLEETVSCFADNPENILAWLGPAIGPRAFEVGGEVREAFmAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRmASFIWLI 243
                                    11        21        31        41        51        61        71        |- |      91       101 |     111       121       131       141       151       161       171 |     181       191       201       211       221       231    |  241  
                                                                                                         80 83                 103-MSE                                                               173-MSE                                                        236-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Cu-oxidase_4] (6)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YFIH_ECOLI | P33644)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
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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  1z9t
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