2V9L - JenaLib

Title :   L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI ( MUTANT Q6Y-E192A)

Authors :   D. Grueninger, G. E. Schulz

Date :   24 Aug 07 (Deposition) - 15 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.23

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Entropy Index, Metal-Binding, Oligomerization, Zinc, Lyase, Aldolase, Class Ii, Cytoplasm, Cleavage Of L-Rhamnulose-1-Phosphate To Dihydroxyacetoneph Bacterial L-Rhamnose Metabolism, Interface Design, Surface Mutation, 2-Ketose Degradation, Protein-Protein Interface, Rare Sugar, Aggregation, Zinc Enzyme, Fibrillation, Rhamnose Metabolism, Protein Engineering (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Grueninger, N. Treiber, M. O. P. Ziegler, J. W. A. Koetter, M. -S. Schulze, G. E. Schulz
Designed Protein-Protein Association.
Science V. 319 206 2008
PubMed-ID: 18187656 | Reference-DOI: 10.1126/SCIENCE.1150421
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:141 , HIS A:143 , HIS A:212 , PO4 A:1276 , PGO A:1283 , HOH A:2535	BINDING SITE FOR RESIDUE ZN A1275
02	AC2	SOFTWARE	ASN A:29 , GLY A:30 , GLY A:31 , ASN A:32 , GLU A:117 , HIS A:141 , HIS A:143 , HIS A:212 , ZN A:1275 , PGO A:1283 , HOH A:2354 , HOH A:2535	BINDING SITE FOR RESIDUE PO4 A1276
03	AC3	SOFTWARE	ASN A:29 , SER A:75 , GLY A:76 , THR A:115 , SER A:116 , HOH A:2121 , HOH A:2348 , HOH A:2349 , HOH A:2536	BINDING SITE FOR RESIDUE ACT A1277
04	AC4	SOFTWARE	SER A:59 , GLY A:189 , ASP A:191 , HOH A:2352 , HOH A:2538	BINDING SITE FOR RESIDUE ACT A1278
05	AC5	SOFTWARE	TYR A:102 , PRO A:114 , THR A:115 , SER A:116 , LEU A:118 , HOH A:2331 , HOH A:2539 , HOH A:2540	BINDING SITE FOR RESIDUE ACT A1279
06	AC6	SOFTWARE	GLY A:76 , LYS A:77 , PHE A:78 , ASP A:222 , HOH A:2306 , HOH A:2453 , HOH A:2541 , HOH A:2542 , HOH A:2543 , HOH A:2544 , HOH A:2545	BINDING SITE FOR RESIDUE ACT A1280
07	AC7	SOFTWARE	TRP A:25 , GLU A:232 , GLN A:236 , HOH A:2097 , HOH A:2101 , HOH A:2460 , HOH A:2546 , HOH A:2547 , HOH A:2548	BINDING SITE FOR RESIDUE PGO A1281
08	AC8	SOFTWARE	ARG A:80 , GLN A:83 , HOH A:2043 , HOH A:2088 , HOH A:2549	BINDING SITE FOR RESIDUE PGO A1282
09	AC9	SOFTWARE	HIS A:143 , GLU A:171 , HIS A:212 , PHE A:263 , ZN A:1275 , PO4 A:1276 , HOH A:2120 , HOH A:2395 , HOH A:2396 , HOH A:2551	BINDING SITE FOR RESIDUE PGO A1283
10	BC1	SOFTWARE	LEU A:154 , TYR A:242 , MET A:244 , LYS A:248 , HOH A:2552 , HOH A:2553 , HOH A:2554	BINDING SITE FOR RESIDUE PGO A1284
11	BC2	SOFTWARE	PRO A:57 , LEU A:58 , SER A:59 , GLN A:60 , PRO A:61 , ALA A:100 , HOH A:2555 , HOH A:2556	BINDING SITE FOR RESIDUE PGO A1285
12	BC3	SOFTWARE	THR A:250 , GLU A:255 , HOH A:2489 , HOH A:2558	BINDING SITE FOR RESIDUE PGO A1286
13	BC4	SOFTWARE	THR A:158 , GLU A:200 , LYS A:203 , HIS A:204 , HOH A:2405 , HOH A:2428 , HOH A:2559 , HOH A:2560 , HOH A:2561	BINDING SITE FOR RESIDUE PGO A1287
14	BC5	SOFTWARE	ARG A:28 , VAL A:175 , SER A:217 , GLU A:223 , LEU A:227 , HOH A:2456 , HOH A:2562 , HOH A:2564	BINDING SITE FOR RESIDUE PGO A1288

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 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
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Chain A from PDB  Type:PROTEIN  Length:274
 aligned with RHAD_ECOLI | P32169 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:274
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    
           RHAD_ECOLI     1 MQNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 274
               SCOP domains d2v9la_ A: L-rhamnulose-1-phosphate aldolase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2v9lA00 A:1-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------Aldolase_II-2v9lA01 A:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhh....eeee....hhhhh..eeeee....hhhhh..hhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.....hhhhhhhhhhhh..hhhhhh...eee.......hhhhhhhhhhhhh...eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v9l A   1 MQNITYSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDAIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 274
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Legend:		→ Mismatch	(orange background)
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		→ 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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (RHAD_ECOLI | P32169)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008994	rhamnulose-1-phosphate aldolase activity	Catalysis of the reaction: L-rhamnulose 1-phosphate = glycerone phosphate + (S)-lactaldehyde.
biological process
	GO:0019323	pentose catabolic process	The chemical reactions and pathways resulting in the breakdown of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule.
	GO:0019301	rhamnose catabolic process	The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.
	GO:0019299	rhamnose metabolic process	The chemical reactions and pathways involving rhamnose, the hexose 6-deoxy-L-mannose. Rhamnose occurs commonly as a compound of plant glycosides, in polysaccharides of gums and mucilages, and in bacterial polysaccharides. It is also a component of some plant cell wall polysaccharides and frequently acts as the sugar components of flavonoids.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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	2v9l
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1gt7	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI
1ojr	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A)
2uyu	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A88F-E192A)
2uyv	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT Q6Y-E192A)
2v29	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT K15W)
2v2a	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248G-R253A- E254A)
2v2b	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E117S-E192A-K248G- R253A-E254A)
2v9e	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248W-A273S)
2v9f	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248W-A273S)
2v9g	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT Q6Y-L84W-E192A)
2v9i	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248W-L274STOP )
2v9m	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A87M-T109F-E192A)
2v9n	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A88F-E192A)
2v9o	L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A87M-T109F-E192A)

Description