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(-) Description

Title :  CONSERVED HYPOTHETICAL PROTEIN PFU-367848-001 FROM PYROCOCCUS FURIOSUS
 
Authors :  P. Horanyi, W. Tempel, J. Habel, L. Chen, D. Lee, D. Nguyen, S. -H. Chang, Q. Florence, W. Zhou, D. Lin, H. Zhang, J. Praissman, F. E. Jenney Jr. , M. W. W. Adams, Z. -J. Liu, J. P. Rose, B. C. Wang, Southeast Collaborat Structural Genomics (Secsg)
Date :  10 Dec 04  (Deposition) - 25 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Structural Genomics, Conserved Hypothetical Protein, Secsg, Psi, Southeast Collaboratory For Structural Genomics, Protein Structure Initiative, Pyrococcus Furiosus, Pfu-367848-001, Hyperthermophile, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Horanyi, W. Tempel, J. Habel, L. Chen, D. Lee, D. Nguyen, S. -H. Chang Q. Florence, W. Zhou, D. Lin, H. Zhang, J. Praissman, F. E. Jenney Jr. , M. W. W. Adams, Z. -J. Liu, J. P. Rose, B. C. Wang, Southeast Collaboratory For Structural Genomics (Secsg)
Conserved Hypothetical Protein Pfu-367848-001 From Pyrococcus Furiosus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificPYROCOCCUS FURIOSUS
    Organism Taxid2261

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (1x)  CD
Biological Unit 3 (1x)AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 73)

Asymmetric Unit (2, 73)
No.NameCountTypeFull Name
1MSE31Mod. Amino AcidSELENOMETHIONINE
2UNX42Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 73)
No.NameCountTypeFull Name
1MSE31Mod. Amino AcidSELENOMETHIONINE
2UNX42Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (2, 37)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE
2UNX22Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 3 (2, 36)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2UNX20Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (42, 42)

Asymmetric Unit (42, 42)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU D:97 , ASP D:98 , THR D:101 , TYR D:120 , UNX D:325 , UNX D:332BINDING SITE FOR RESIDUE UNX D 301
02AC2SOFTWAREASP C:10 , SER C:11 , THR C:41 , GLU C:97 , THR C:101BINDING SITE FOR RESIDUE UNX C 302
03AC3SOFTWAREASP A:10 , SER A:11 , THR A:41 , GLU A:97 , THR A:101BINDING SITE FOR RESIDUE UNX A 303
04AC4SOFTWARESER B:38 , VAL B:70 , PRO B:71 , THR B:104BINDING SITE FOR RESIDUE UNX B 304
05AC5SOFTWAREASP C:10 , ALA C:13 , THR C:114 , ASP C:115BINDING SITE FOR RESIDUE UNX C 305
06AC6SOFTWARETHR C:8 , ASN C:36 , THR C:104 , ALA C:105 , THR C:108 , UNX C:308BINDING SITE FOR RESIDUE UNX C 306
07AC7SOFTWAREASP B:98 , THR B:101 , ARG B:119 , TYR B:120 , UNX B:323 , UNX B:328BINDING SITE FOR RESIDUE UNX B 307
08AC8SOFTWARETHR C:8 , THR C:101 , THR C:104 , ALA C:105 , UNX C:306 , UNX C:311BINDING SITE FOR RESIDUE UNX C 308
09AC9SOFTWARETHR D:8 , PHE D:9 , SER D:38 , THR D:41 , UNX D:322BINDING SITE FOR RESIDUE UNX D 309
10BC1SOFTWARETHR A:8 , THR A:101 , THR A:104 , ALA A:105 , UNX A:312 , UNX A:317BINDING SITE FOR RESIDUE UNX A 310
11BC2SOFTWARETHR C:8 , PHE C:9 , SER C:38 , THR C:41 , UNX C:308BINDING SITE FOR RESIDUE UNX C 311
12BC3SOFTWARETHR A:8 , PHE A:9 , SER A:38 , THR A:41 , UNX A:310BINDING SITE FOR RESIDUE UNX A 312
13BC4SOFTWARESER A:38 , VAL A:70 , PRO A:71 , THR A:104BINDING SITE FOR RESIDUE UNX A 313
14BC5SOFTWARESER C:38 , VAL C:70 , PRO C:71 , THR C:104BINDING SITE FOR RESIDUE UNX C 314
15BC6SOFTWARETHR B:8 , THR B:101 , ALA B:105 , UNX B:320 , UNX B:329BINDING SITE FOR RESIDUE UNX B 315
16BC7SOFTWAREASP C:95 , ILE C:96 , GLU C:97 , UNX C:324BINDING SITE FOR RESIDUE UNX C 316
17BC8SOFTWARETHR A:8 , ASN A:36 , THR A:104 , ALA A:105 , THR A:108 , UNX A:310BINDING SITE FOR RESIDUE UNX A 317
18BC9SOFTWAREASP B:10 , LEU B:12 , ALA B:13 , THR B:114 , ASP B:115BINDING SITE FOR RESIDUE UNX B 318
19CC1SOFTWAREASP C:95 , ILE C:96BINDING SITE FOR RESIDUE UNX C 319
20CC2SOFTWARETHR B:8 , PHE B:9 , SER B:38 , THR B:41 , UNX B:315BINDING SITE FOR RESIDUE UNX B 320
21CC3SOFTWARESER D:38 , VAL D:70 , PRO D:71 , LEU D:72 , THR D:104BINDING SITE FOR RESIDUE UNX D 321
22CC4SOFTWARETHR D:8 , THR D:101 , THR D:104 , ALA D:105 , UNX D:309 , UNX D:327BINDING SITE FOR RESIDUE UNX D 322
23CC5SOFTWAREASP B:10 , SER B:11 , THR B:41 , GLU B:97 , THR B:101 , UNX B:307 , UNX B:328BINDING SITE FOR RESIDUE UNX B 323
24CC6SOFTWAREGLU C:97 , UNX C:316BINDING SITE FOR RESIDUE UNX C 324
25CC7SOFTWAREASP D:10 , SER D:11 , THR D:41 , GLU D:97 , THR D:101 , UNX D:301 , UNX D:332BINDING SITE FOR RESIDUE UNX D 325
26CC8SOFTWAREASP D:10 , LEU D:12 , ALA D:13 , THR D:114 , ASP D:115 , UNX D:337BINDING SITE FOR RESIDUE UNX D 326
27CC9SOFTWARETHR D:8 , ASN D:36 , THR D:104 , ALA D:105 , THR D:108 , UNX D:322BINDING SITE FOR RESIDUE UNX D 327
28DC1SOFTWAREASP B:10 , SER B:11 , GLU B:97 , ARG B:119 , UNX B:307 , UNX B:323BINDING SITE FOR RESIDUE UNX B 328
29DC2SOFTWARETHR B:8 , ASN B:36 , THR B:104 , ALA B:105 , THR B:108 , UNX B:315BINDING SITE FOR RESIDUE UNX B 329
30DC3SOFTWAREGLU A:97 , UNX A:334BINDING SITE FOR RESIDUE UNX A 330
31DC4SOFTWAREASP C:10 , SER C:11 , LEU C:12 , UNX C:341 , UNX C:342BINDING SITE FOR RESIDUE UNX C 331
32DC5SOFTWARESER D:11 , GLU D:97 , ARG D:119 , UNX D:301 , UNX D:325 , UNX D:340BINDING SITE FOR RESIDUE UNX D 332
33DC6SOFTWAREASP A:10 , SER A:11 , LEU A:12BINDING SITE FOR RESIDUE UNX A 333
34DC7SOFTWAREASP A:95 , ILE A:96 , GLU A:97 , UNX A:330 , ILE B:96BINDING SITE FOR RESIDUE UNX A 334
35DC8SOFTWAREGLU A:97 , ASP A:98 , TYR A:120BINDING SITE FOR RESIDUE UNX A 335
36DC9SOFTWAREGLU A:84 , PRO A:94 , ASP A:95 , ILE A:96 , TYR B:43BINDING SITE FOR RESIDUE UNX A 336
37EC1SOFTWAREASP D:10 , ARG D:119 , UNX D:326 , UNX D:340BINDING SITE FOR RESIDUE UNX D 337
38EC2SOFTWAREASP B:95 , ASP B:98 , ARG B:119BINDING SITE FOR RESIDUE UNX B 338
39EC3SOFTWAREASP A:95 , ILE A:96BINDING SITE FOR RESIDUE UNX A 339
40EC4SOFTWAREASP D:10 , SER D:11 , LEU D:12 , ARG D:119 , UNX D:332 , UNX D:337BINDING SITE FOR RESIDUE UNX D 340
41EC5SOFTWAREASP C:10 , TYR C:120 , UNX C:331BINDING SITE FOR RESIDUE UNX C 341
42EC6SOFTWARESER C:11 , ARG C:44 , GLU C:97 , UNX C:331BINDING SITE FOR RESIDUE UNX C 342

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y82)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y82)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y82)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y82)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y82)

(-) 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:147
 aligned with Y355_PYRFU | Q8U3V0 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           Y355_PYRFU     2 PLPPDITFDSLALIKMHSQSMKKILEITLAKFTVNLSIVTVYRYLTVRAYLKKNIELELDVLKDIYNIVPLNEEIAIKAAQIEADLMRKGMMPDIEDVLTAATAIYTKSLLITDDSKRYEPMRRFGLDTMPLDKFVKEVELMVEKEL 148
               SCOP domains d1y82a1 A:2-148 Hypothetical protein PF0355                                                                                                         SCOP domains
               CATH domains 1y82A00 A:2-148 5'-nuclease                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhh..hhhhhhhhhhhhheee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhh..eeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y82 A   2 PLPPDITFDSLALIKmHSQSmKKILEITLAKFTVNLSIVTVYRYLTVRAYLKKNIELELDVLKDIYNIVPLNEEIAIKAAQIEADLmRKGmmPDIEDVLTAATAIYTKSLLITDDSKRYEPmRRFGLDTmPLDKFVKEVELmVEKEL 148
                                    11     |  21|       31        41        51        61        71        81      | 91||     101       111       121 |     131       141 |     
                                          17-MSE|                                                                88-MSE|                           123-MSE 131-MSE     143-MSE 
                                               22-MSE                                                                92-MSE                                                    
                                                                                                                      93-MSE                                                   

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with Y355_PYRFU | Q8U3V0 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142      
           Y355_PYRFU     3 LPPDITFDSLALIKMHSQSMKKILEITLAKFTVNLSIVTVYRYLTVRAYLKKNIELELDVLKDIYNIVPLNEEIAIKAAQIEADLMRKGMMPDIEDVLTAATAIYTKSLLITDDSKRYEPMRRFGLDTMPLDKFVKEVELMVEKEL 148
               SCOP domains d1y82b_ B: Hypothetical protein PF0355                                                                                                             SCOP domains
               CATH domains 1y82B00 B:3-148 5'-nuclease                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhh..hhhhhhhhhhhheeeeehhhhhhhhhhhhhh..hhhhhhhhhhhhheee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee..hhhhhhhhhhh..eeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y82 B   3 LPPDITFDSLALIKmHSQSmKKILEITLAKFTVNLSIVTVYRYLTVRAYLKKNIELELDVLKDIYNIVPLNEEIAIKAAQIEADLmRKGmmPDIEDVLTAATAIYTKSLLITDDSKRYEPmRRFGLDTmPLDKFVKEVELmVEKEL 148
                                    12    |   22        32        42        52        62        72        82     |  92|      102       112       122|      132       142|     
                                         17-MSE|                                                                88-MSE|                           123-MSE 131-MSE     143-MSE 
                                              22-MSE                                                                92-MSE                                                    
                                                                                                                     93-MSE                                                   

Chain C from PDB  Type:PROTEIN  Length:146
 aligned with Y355_PYRFU | Q8U3V0 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142      
           Y355_PYRFU     3 LPPDITFDSLALIKMHSQSMKKILEITLAKFTVNLSIVTVYRYLTVRAYLKKNIELELDVLKDIYNIVPLNEEIAIKAAQIEADLMRKGMMPDIEDVLTAATAIYTKSLLITDDSKRYEPMRRFGLDTMPLDKFVKEVELMVEKEL 148
               SCOP domains d1y82c_ C: Hypothetical protein PF0355                                                                                                             SCOP domains
               CATH domains 1y82C00 C:3-148 5'-nuclease                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhh..hhhhhhhhhhhhheee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.eeee.....hhhhhhhh..eeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y82 C   3 LPPDITFDSLALIKmHSQSmKKILEITLAKFTVNLSIVTVYRYLTVRAYLKKNIELELDVLKDIYNIVPLNEEIAIKAAQIEADLmRKGmmPDIEDVLTAATAIYTKSLLITDDSKRYEPmRRFGLDTmPLDKFVKEVELmVEKEL 148
                                    12    |   22        32        42        52        62        72        82     |  92|      102       112       122|      132       142|     
                                         17-MSE|                                                                88-MSE|                           123-MSE 131-MSE     143-MSE 
                                              22-MSE                                                                92-MSE                                                    
                                                                                                                     93-MSE                                                   

Chain D from PDB  Type:PROTEIN  Length:139
 aligned with Y355_PYRFU | Q8U3V0 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132         
           Y355_PYRFU     3 LPPDITFDSLALIKMHSQSMKKILEITLAKFTVNLSIVTVYRYLTVRAYLKKNIELELDVLKDIYNIVPLNEEIAIKAAQIEADLMRKGMMPDIEDVLTAATAIYTKSLLITDDSKRYEPMRRFGLDTMPLDKFVKEVE 141
               SCOP domains d1y82d_ D: Hypothetical protein PF0355                                                                                                      SCOP domains
               CATH domains 1y82D00 D:3-141 5'-nuclease                                                                                                                 CATH domains
           Pfam domains (1) ----PIN-1y82D01 D:7-126                                                                                                     --------------- Pfam domains (1)
           Pfam domains (2) ----PIN-1y82D02 D:7-126                                                                                                     --------------- Pfam domains (2)
           Pfam domains (3) ----PIN-1y82D03 D:7-126                                                                                                     --------------- Pfam domains (3)
           Pfam domains (4) ----PIN-1y82D04 D:7-126                                                                                                     --------------- Pfam domains (4)
         Sec.struct. author ...eeeehhhhhhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhh..hhhhhhhhhhhhheee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh..eeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y82 D   3 LPPDITFDSLALIKmHSQSmKKILEITLAKFTVNLSIVTVYRYLTVRAYLKKNIELELDVLKDIYNIVPLNEEIAIKAAQIEADLmRKGmmPDIEDVLTAATAIYTKSLLITDDSKRYEPmRRFGLDTmPLDKFVKEVE 141
                                    12    |   22        32        42        52        62        72        82     |  92|      102       112       122|      132         
                                         17-MSE|                                                                88-MSE|                           123-MSE 131-MSE      
                                              22-MSE                                                                92-MSE                                             
                                                                                                                     93-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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PIN (27)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Y355_PYRFU | Q8U3V0)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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  Y355_PYRFU | Q8U3V0
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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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