4R2X - JenaLib

Title :   UNIQUE CONFORMATION OF URIDINE AND ASYMMETRY OF THE HEXAMERIC MOLECULE REVEALED IN THE HIGH-RESOLUTION STRUCTURES OF SHEWANELLA ONEIDENSIS URIDINE PHOSPHORYLASE IN THE FREE FORM AND IN COMPLEX WITH URIDINE

Authors :   T. N. Safonova, N. N. Mordkovich, V. A. Manuvera, V. P. Veiko, V. O. Popov K. M. Polyakov

Date :   13 Aug 14 (Deposition) - 10 Dec 14 (Release) - 07 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.93

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Uridine Phosphorylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. N. Safonova, S. N. Mikhailov, V. P. Veiko, N. N. Mordkovich, V. A. Manuvera, C. S. Alekseev, M. V. Kovalchuk, V. O. Popov, K. M. Polyakov
High-Syn Conformation Of Uridine And Asymmetry Of The Hexameric Molecule Revealed In The High-Resolution Structures Of Shewanella Oneidensis Mr-1 Uridine Phosphorylase In The Free Form And In Complex With Uridine.
Acta Crystallogr. , Sect. D V. 70 3310 2014
PubMed-ID: 25478848 | Reference-DOI: 10.1107/S1399004714024079

Compounds

Molecule 1 - URIDINE PHOSPHORYLASE
	Chains	:	C, D, E, F, A, B
	EC Number	:	2.4.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UDP, SO_4133
	Organism Scientific	:	SHEWANELLA ONEIDENSIS
	Organism Taxid	:	211586
	Strain	:	MR-1

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 31)

Sites (31, 31)

Asymmetric Unit (31, 31)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY C:23 , ARG C:27 , ARG C:88 , VAL C:89 , GLY C:90 , THR C:91 , GOL C:303 , ARG D:45	BINDING SITE FOR RESIDUE SO4 C 301
02	AC2	SOFTWARE	GLY C:93 , GLN C:163 , ARG C:165 , HOH C:434 , HOH C:485	BINDING SITE FOR RESIDUE CL C 302
03	AC3	SOFTWARE	ILE C:66 , ARG C:88 , THR C:91 , GLU C:193 , MET C:194 , GLU C:195 , SO4 C:301 , HOH C:436 , HOH C:485 , ARG D:45 , HOH D:461	BINDING SITE FOR RESIDUE GOL C 303
04	AC4	SOFTWARE	ASN C:130 , ALA C:204 , HOH C:405 , HOH C:411 , HOH C:435 , HOH C:465 , HOH C:482 , HOH C:587	BINDING SITE FOR RESIDUE GOL C 304
05	AC5	SOFTWARE	ARG C:176 , GLU C:183 , HOH C:452 , ARG E:175 , PRO F:122 , GLU F:124	BINDING SITE FOR RESIDUE GOL C 305
06	AC6	SOFTWARE	ALA C:140 , ASP C:143 , ALA C:144 , ALA C:244 , LYS C:248 , HOH C:441 , HOH C:513	BINDING SITE FOR RESIDUE GOL C 306
07	AC7	SOFTWARE	ARG C:45 , GLY D:23 , ARG D:27 , ARG D:88 , VAL D:89 , GLY D:90 , THR D:91 , GOL D:303	BINDING SITE FOR RESIDUE SO4 D 301
08	AC8	SOFTWARE	GLY D:93 , GLN D:163 , ARG D:165 , HOH D:403 , HOH D:460	BINDING SITE FOR RESIDUE CL D 302
09	AC9	SOFTWARE	ARG C:45 , HOH C:455 , ILE D:66 , ARG D:88 , THR D:91 , GLU D:193 , MET D:194 , GLU D:195 , SO4 D:301 , HOH D:452 , HOH D:460	BINDING SITE FOR RESIDUE GOL D 303
10	BC1	SOFTWARE	PRO A:122 , GLU A:124 , ARG B:175 , ARG D:176 , GLU D:183 , HOH D:468 , HOH D:560	BINDING SITE FOR RESIDUE GOL D 304
11	BC2	SOFTWARE	ASN D:130 , ALA D:204 , HOH D:407 , HOH D:420 , HOH D:429 , HOH D:450 , HOH D:476 , HOH D:597	BINDING SITE FOR RESIDUE GOL D 305
12	BC3	SOFTWARE	ARG A:175 , ARG C:175 , ARG E:175 , HOH E:519 , HOH E:541	BINDING SITE FOR RESIDUE SO4 E 301
13	BC4	SOFTWARE	ILE E:66 , ARG E:88 , THR E:91 , GLU E:193 , MET E:194 , GLU E:195 , SO4 E:303 , HOH E:449 , HOH E:562	BINDING SITE FOR RESIDUE GOL E 302
14	BC5	SOFTWARE	GLY E:23 , ARG E:27 , ARG E:88 , VAL E:89 , GLY E:90 , THR E:91 , GOL E:302 , HOH E:554 , HOH E:561 , HOH E:562 , ARG F:45	BINDING SITE FOR RESIDUE SO4 E 303
15	BC6	SOFTWARE	ASN E:130 , ALA E:204 , HOH E:409 , HOH E:419 , HOH E:421 , HOH E:422 , HOH E:475 , HOH E:548	BINDING SITE FOR RESIDUE GOL E 304
16	BC7	SOFTWARE	ARG A:175 , PRO B:122 , GLU B:124 , ARG E:176 , GLU E:183 , HOH E:437 , HOH E:543 , HOH E:550	BINDING SITE FOR RESIDUE GOL E 305
17	BC8	SOFTWARE	ARG E:45 , GLY F:23 , ARG F:27 , ARG F:88 , VAL F:89 , GLY F:90 , THR F:91 , GOL F:305	BINDING SITE FOR RESIDUE SO4 F 301
18	BC9	SOFTWARE	GLY F:93 , GLN F:163 , ARG F:165 , HOH F:413 , HOH F:452	BINDING SITE FOR RESIDUE CL F 302
19	CC1	SOFTWARE	PRO C:122 , GLU C:124 , ARG D:175 , LEU F:113 , ARG F:176 , GLU F:183 , HOH F:454	BINDING SITE FOR RESIDUE GOL F 303
20	CC2	SOFTWARE	ASN F:130 , ALA F:204 , HOH F:410 , HOH F:411 , HOH F:429 , HOH F:437 , HOH F:457 , HOH F:527	BINDING SITE FOR RESIDUE GOL F 304
21	CC3	SOFTWARE	ARG E:45 , HOH E:482 , ILE F:66 , ARG F:88 , THR F:91 , GLU F:193 , MET F:194 , GLU F:195 , SO4 F:301 , HOH F:433 , HOH F:452	BINDING SITE FOR RESIDUE GOL F 305
22	CC4	SOFTWARE	GLY A:23 , ARG A:27 , ARG A:88 , VAL A:89 , GLY A:90 , THR A:91 , GOL A:303 , ARG B:45	BINDING SITE FOR RESIDUE SO4 A 301
23	CC5	SOFTWARE	GLY A:93 , GLN A:163 , ARG A:165 , HOH A:456	BINDING SITE FOR RESIDUE CL A 302
24	CC6	SOFTWARE	ILE A:66 , ARG A:88 , THR A:91 , GLU A:193 , MET A:194 , GLU A:195 , SO4 A:301 , HOH A:419 , HOH A:456 , ARG B:45 , HOH B:455	BINDING SITE FOR RESIDUE GOL A 303
25	CC7	SOFTWARE	ASN A:130 , ALA A:204 , HOH A:421 , HOH A:427 , HOH A:433 , HOH A:443 , HOH A:501 , HOH A:550	BINDING SITE FOR RESIDUE GOL A 304
26	CC8	SOFTWARE	ARG A:176 , GLU A:183 , HOH A:471 , HOH A:525 , HOH A:584 , ARG C:175 , PRO D:122 , GLU D:124	BINDING SITE FOR RESIDUE GOL A 305
27	CC9	SOFTWARE	ARG B:175 , HOH B:490 , HOH B:527 , HOH B:530 , HOH B:561 , ARG D:175 , ARG F:175	BINDING SITE FOR RESIDUE SO4 B 301
28	DC1	SOFTWARE	ASN B:130 , ALA B:204 , HOH B:408 , HOH B:409 , HOH B:416 , HOH B:453 , HOH B:469 , HOH B:548	BINDING SITE FOR RESIDUE GOL B 302
29	DC2	SOFTWARE	ILE B:66 , ARG B:88 , GLU B:193 , MET B:194 , GLU B:195 , SO4 B:304 , HOH B:441 , HOH B:518 , HOH B:532	BINDING SITE FOR RESIDUE GOL B 303
30	DC3	SOFTWARE	ARG A:45 , GLY B:23 , ARG B:27 , ARG B:88 , VAL B:89 , GLY B:90 , THR B:91 , GOL B:303 , HOH B:532	BINDING SITE FOR RESIDUE SO4 B 304
31	DC4	SOFTWARE	LEU B:113 , ARG B:176 , SER B:180 , GLU B:183 , TRP B:184 , HOH B:444 , HOH B:549 , HOH B:552 , HOH B:558 , PRO E:122 , GLU E:124 , ARG F:175	BINDING SITE FOR RESIDUE GOL B 305

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeeee.hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh....eeeeeeee...hhhhh..............hhhhhhhhh...eee.hhhhhhhhhhhhh.eeeeeeeeeee........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r2x A   1 ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQQEIPSAVSIVVAAAKKLLA 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     ||240       250 
                                                                                                                                                                                                                                                           226|              
                                                                                                                                                                                                                                                            237

Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhh...eee...hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh....eeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh.eeeeeeeeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r2x B   1 ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQTEVSAVSIVVAAAKKLLA 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 ||    241       251
                                                                                                                                                                                                                                                       222|                 
                                                                                                                                                                                                                                                        234

Chain C from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...eeeee.hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh....eeeeeeee...hhhhh..............hhhhhhhhh...eee.hhhhhhhhhhhhh.eeeeeeeeeee.............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r2x C   1 ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQQEIPDEATMVSAVSIVVAAAKKLLA 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230||     244       
                                                                                                                                                                                                                                                                231|               
                                                                                                                                                                                                                                                                 236

Chain D from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...eeeee.hhhhhhhhhhh.eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh....eeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh.eeeeeeeeeee...............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r2x D   1 ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQQEIPDEATMKEVSAVSIVVAAAKKLLA 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 ||    242         
                                                                                                                                                                                                                                                                 232|                
                                                                                                                                                                                                                                                                  235

Chain E from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...eee...hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh....eeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh.eeeeeeeeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r2x E   1 ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQKTEVSAVSIVVAAAKKLLA 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 ||    240       250 
                                                                                                                                                                                                                                                       222|                  
                                                                                                                                                                                                                                                        233

Chain F from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeeee.hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh....eeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhh.eeeeeeeeeee........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r2x F   1 ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQQEIPVSAVSIVVAAAKKLLA 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     ||239       249  
                                                                                                                                                                                                                                                           226|               
                                                                                                                                                                                                                                                            236

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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 '\|'

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