4HFQ - JenaLib

Title :   CRYSTAL STRUCTURE OF UDP-X DIPHOSPHATASE

Authors :   K. C. Duong-Ly, L. M. Amzel, S. B. Gabelli

Date :   05 Oct 12 (Deposition) - 07 Aug 13 (Release) - 07 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.39

Chains :   Asym./Biol. Unit : A,B

Keywords :   Udp-Sugar Diphosphatase, Nudix, Hydrolase, Rna Exonuclease, Pyrophosphatase, Mur Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. C. Duong-Ly, H. N. Woo, C. A. Dunn, W. Xu, A. Babic, M. J. Bessman, L. M. Amzel, S. B. Gabelli
A Udp-X Diphosphatase From Streptococcus Pneumoniae Hydrolyzes Precursors Of Peptidoglycan Biosynthesis.
Plos One V. 8 64241 2013
PubMed-ID: 23691178 | Reference-DOI: 10.1371/JOURNAL.PONE.0064241

Compounds

Molecule 1 - MUTT/NUDIX FAMILY PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-24A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SP1669, SP_1669
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	170187
	Strain	:	TIGR4

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 30)

Asymmetric/Biological Unit (6, 30)

No.	Name	Count	Type	Full Name
1	EDO	11	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	6	Ligand/Ion	GLYCEROL
3	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
5	SO4	5	Ligand/Ion	SULFATE ION
6	TRS	3	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Sites (30, 30)

Asymmetric Unit (30, 30)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:177 , SER A:178 , GLU A:179 , LYS A:180 , PEG A:310 , HOH A:464	BINDING SITE FOR RESIDUE EDO A 301
02	AC2	SOFTWARE	ASP A:5 , TYR A:9 , HOH A:632	BINDING SITE FOR RESIDUE EDO A 302
03	AC3	SOFTWARE	ASP A:71 , ARG A:73 , GLN A:139 , TYR A:143 , LYS A:145 , LYS A:180 , ARG A:181 , HOH A:427 , HOH A:578 , PRO B:61	BINDING SITE FOR RESIDUE TRS A 303
04	AC4	SOFTWARE	ARG A:73 , VAL A:85 , GLY A:97 , GLU A:117 , GLU A:162 , ARG A:181 , HOH A:430 , HOH A:442 , HOH A:593	BINDING SITE FOR RESIDUE SO4 A 304
05	AC5	SOFTWARE	ARG A:86 , TRP A:191 , GLN A:192 , GLN A:195 , HIS A:197 , HOH A:413 , HOH A:616 , HOH A:617	BINDING SITE FOR RESIDUE SO4 A 305
06	AC6	SOFTWARE	GLU A:101 , TYR A:104 , LYS A:112 , LYS B:8 , ARG B:12 , HOH B:509	BINDING SITE FOR RESIDUE SO4 A 306
07	AC7	SOFTWARE	LEU A:111 , LYS A:112 , GLU A:115 , LYS A:121 , ALA A:122 , HOH A:445 , HOH A:446 , HOH A:470	BINDING SITE FOR RESIDUE PEG A 307
08	AC8	SOFTWARE	LYS A:8 , ASN A:134 , HOH A:420 , HOH B:571	BINDING SITE FOR RESIDUE EDO A 308
09	AC9	SOFTWARE	ARG A:135 , ASP A:203 , HOH A:438 , HOH A:605 , HOH A:633 , SER B:105 , GLU B:108	BINDING SITE FOR RESIDUE GOL A 309
10	BC1	SOFTWARE	ASN A:176 , LEU A:177 , GLU A:179 , LYS A:184 , EDO A:301 , HOH A:414 , HOH A:462 , HOH A:629	BINDING SITE FOR RESIDUE PEG A 310
11	BC2	SOFTWARE	LYS A:2 , THR A:3 , SER A:4 , HOH A:498 , HOH A:508	BINDING SITE FOR RESIDUE SO4 A 311
12	BC3	SOFTWARE	ALA A:66 , HOH A:429 , HOH A:485 , HOH A:511 , PHE B:99 , GLY B:100 , GLU B:101	BINDING SITE FOR RESIDUE EDO A 312
13	BC4	SOFTWARE	THR A:62 , SER A:63 , TYR A:65 , ALA A:66 , THR A:67 , LEU A:69 , LYS A:141 , GLN A:142 , HOH A:412 , HOH A:416 , HOH A:502 , HOH A:584 , LEU B:69 , VAL B:102	BINDING SITE FOR RESIDUE PGE A 313
14	BC5	SOFTWARE	SER A:63 , VAL A:102 , HOH A:507 , ALA B:15 , LEU B:69 , LYS B:141 , GLN B:142 , HOH B:415 , HOH B:441	BINDING SITE FOR RESIDUE GOL A 314
15	BC6	SOFTWARE	GLU A:78 , PHE A:120 , LEU A:152 , PHE A:168 , HOH A:532 , HOH A:534 , HOH A:590	BINDING SITE FOR RESIDUE GOL A 315
16	BC7	SOFTWARE	ASP A:91 , TRP A:93 , GLN A:167 , ASN A:176 , EDO A:317 , HOH A:408	BINDING SITE FOR RESIDUE PEG A 316
17	BC8	SOFTWARE	ASP A:91 , ASN A:176 , LEU A:189 , GLN A:192 , ARG A:198 , PEG A:316 , HOH A:408	BINDING SITE FOR RESIDUE EDO A 317
18	BC9	SOFTWARE	GLN B:139 , SER B:140 , LYS B:180 , EDO B:302 , HOH B:432 , HOH B:461	BINDING SITE FOR RESIDUE SO4 B 301
19	CC1	SOFTWARE	ASN B:45 , LEU B:138 , SO4 B:301 , HOH B:528 , HOH B:530	BINDING SITE FOR RESIDUE EDO B 302
20	CC2	SOFTWARE	ARG B:73 , GLN B:139 , TYR B:143 , LYS B:145 , LYS B:180 , ARG B:181 , TRS B:305 , HOH B:477 , HOH B:626	BINDING SITE FOR RESIDUE GOL B 303
21	CC3	SOFTWARE	GLU B:78 , PHE B:120 , PHE B:168 , HOH B:438 , HOH B:534 , HOH B:543 , HOH B:640	BINDING SITE FOR RESIDUE GOL B 304
22	CC4	SOFTWARE	ARG B:73 , GLY B:97 , GLU B:117 , GLU B:162 , ILE B:163 , ARG B:181 , GOL B:303 , HOH B:439 , HOH B:477 , HOH B:596 , HOH B:633	BINDING SITE FOR RESIDUE TRS B 305
23	CC5	SOFTWARE	PRO A:68 , LEU A:69 , MET A:70 , THR A:144 , PRO B:68 , MET B:70 , THR B:144 , PHE B:146 , HOH B:544	BINDING SITE FOR RESIDUE EDO B 306
24	CC6	SOFTWARE	LYS A:123 , LEU B:177 , SER B:178 , GLU B:179 , LYS B:180 , HOH B:559 , HOH B:604 , HOH B:615	BINDING SITE FOR RESIDUE TRS B 307
25	CC7	SOFTWARE	ARG A:12 , GLU B:31 , ASP B:35 , GLU B:101 , LYS B:112 , GLU B:116 , HOH B:417 , HOH B:525	BINDING SITE FOR RESIDUE GOL B 308
26	CC8	SOFTWARE	LEU A:21 , THR A:22 , HOH B:446 , HOH B:618 , HOH B:620	BINDING SITE FOR RESIDUE EDO B 309
27	CC9	SOFTWARE	ARG A:30 , HOH A:441 , THR B:24 , LYS B:25 , PRO B:27 , ARG B:30 , HOH B:516	BINDING SITE FOR RESIDUE EDO B 310
28	DC1	SOFTWARE	LEU B:202 , PEG B:313 , HOH B:542 , HOH B:643	BINDING SITE FOR RESIDUE EDO B 311
29	DC2	SOFTWARE	ARG B:86 , TRP B:93 , GLY B:196 , ARG B:198 , GLY B:199 , HOH B:428	BINDING SITE FOR RESIDUE EDO B 312
30	DC3	SOFTWARE	LEU B:174 , PRO B:175 , ARG B:198 , GLY B:199 , GLN B:200 , TYR B:201 , LEU B:202 , EDO B:311 , HOH B:440 , HOH B:567	BINDING SITE FOR RESIDUE PEG B 313

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........eeeeeee.ee..eeeeeee.....ee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeehhhhh.....eeeeeeeeeeeee.......eeeeeeee............hhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hfq A   1 MKTSDFVKYLQRMIAITDTGLTFTKDPFDRERYEDLRSLLSEMLNQASDLDSEEVAEVLKPTSAYATPLMDVRAWIVEDEKICLVRGQGEDSWALPGGFGEVGYSPTENILKEIEEETGFKAKVERLLAVFDTNRFQLQSKQYTKFVFGCKLLDGQFQENQEIADLQFFAIDQLPNLSEKRITKEQIELLWQVYQGHRGQYLD 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh........eeeeeee.ee..eeeeeee.....ee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeehhhhh.....eeeeeeeeeeeee.......eeeeeeehhhhh........hhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hfq B   1 MKTSDFVKYLQRMIAITDTGLTFTKDPFDRERYEDLRSLLSEMLNQASDLDSEEVAEVLKPTSAYATPLMDVRAWIVEDEKICLVRGQGEDSWALPGGFGEVGYSPTENILKEIEEETGFKAKVERLLAVFDTNRFQLQSKQYTKFVFGCKLLDGQFQENQEIADLQFFAIDQLPNLSEKRITKEQIELLWQVYQGHRGQYLD 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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Description